Submissions for variant NM_000492.3(CFTR):c.1521_1523del (p.Phe508del)

dbSNP: rs113993960

Total submissions: 90

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
American College of Medical Genetics and Genomics (ACMG)	RCV000007523	SCV000071392	pathogenic	Cystic fibrosis	2004-03-03	practice guideline	curation	Converted during submission to Pathogenic.
CFTR2	RCV000007523	SCV000071493	pathogenic	Cystic fibrosis	2017-03-17	reviewed by expert panel	research
PharmGKB	RCV001787370	SCV002031250	drug response	ivacaftor / lumacaftor response - Efficacy	2021-03-24	reviewed by expert panel	curation	PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance.
PharmGKB	RCV001787371	SCV002031251	drug response	ivacaftor / tezacaftor response - Efficacy	2021-03-24	reviewed by expert panel	curation	PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000007523	SCV000074347	pathogenic	Cystic fibrosis	2024-01-31	criteria provided, single submitter	clinical testing	This variant, c.1521_1523del, results in the deletion of 1 amino acid(s) of the CFTR protein (p.Phe508del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs199826652, gnomAD 1.2%), including at least one homozygous and/or hemizygous individual. This variant has been observed in individual(s) with cystic fibrosis and is the most common cause of the condition (PMID: 2475911, 15371902, 23974870). It has also been observed to segregate with disease in related individuals. This variant is also known as ∆F508. ClinVar contains an entry for this variant (Variation ID: 7105). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects CFTR function (PMID: 2475911, 23974870). For these reasons, this variant has been classified as Pathogenic.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000007523	SCV000221179	pathogenic	Cystic fibrosis	2022-11-03	criteria provided, single submitter	clinical testing	The p.Phe508del variant in CFTR (also known as ΔF508) is a deletion of a single amino acid at position 508 and is well-established as a pathogenic variant for autosomal recessive cystic fibrosis (Kerem 1989 PMID:2570460, Fuller 1992 PMID:1381146, Southern 1997 PMID:9135274, Grody 2001 PMID:11280952, Sosnay 2013 PMID:23974870). This is the most common pathogenic variant reported in CFTR and has been classified as Pathogenic by the ACMG practice guideline for cystic fibrosis carrier screening and the ClinGen-approved CFTR2 expert panel (ClinVar Variation ID 7105). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive cystic fibrosis. ACMG/AMP Criteria applied: PM3_Very Strong, PP1_Strong, PS3, PM4_Supporting.
GeneDx	RCV000058929	SCV000329246	pathogenic	not provided	2018-07-30	criteria provided, single submitter	clinical testing	The c.1521_1523delCTT pathogenic variant in the CFTR gene (also known as p.Phe508del or delta F508) is the most common variant identified in the CFTR gene, with up to 90% of individuals with cystic fibrosis (CF) having at least one copy of the c.1521_1523delCTT variant (Cai et al., 2011). The c.1521_1523delCTT variant results in an in-frame deletion of a single Phenylalanine residue at codon 508. Individuals who are homozygous for the c.1521_1523delCTT variant demonstrate the classic features of CF, whereas individuals compound heterozygous for the c.1521_1523delCTT variant and another CFTR variant may have a modified disease phenotype (Ong et al., 2017). Heterozygous carriers of the c.1521_1523delCTT variant are usually asymptomatic, however, may be at increased risk for developing a CFTR-related disorder, as an increased prevalence of single CFTR pathogenic variants has been observed among individuals with chronic pulmonary conditions, CAVD and pancreatitis (Cuppens et al., 2004; Bombieri et al., 2011). We interpret the c.1521_1523delCTT variant as a pathogenic variant.
Eurofins Ntd Llc (ga)	RCV000058929	SCV000330918	pathogenic	not provided	2017-01-03	criteria provided, single submitter	clinical testing
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	RCV000058929	SCV000511517	pathogenic	not provided	2016-10-28	criteria provided, single submitter	clinical testing
Knight Diagnostic Laboratories, Oregon Health and Sciences University	RCV000007523	SCV000538017	pathogenic	Cystic fibrosis	2016-03-30	criteria provided, single submitter	clinical testing	The c.1521_1523delCTT (p.Phe508del), also known as ΔF508, is an in-frame deletion in the CFTR gene. This variant is the most common CF-causing mutation, accounting for an estimated 72% of mutant alleles in people of European ancestry (Watson et al., 2004). This p.Phe508del variant is classified as a class II mutation that blocks the processing of the CFTR protein (Welsh et al., 2001). This variant has been reported at low frequencies (1.0%) in 1000 Genomes and ExAc population databases, but has not been reported in the Exome Sequencing Project database (ESP). The CFTR2 database has 32,833 patients that have this mutation, which they classify as CF-causing (http://www.cftr2.org/mutation.php?view=general&mutation_id=1). Therefore, this collective evidence supports the classification of the c.1521_1523delCTT (p.Phe508del) as a recessive pathogenic variant for Cystic fibrosis.
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	RCV000007523	SCV000584079	pathogenic	Cystic fibrosis	2013-10-21	criteria provided, single submitter	research
Genetic Services Laboratory, University of Chicago	RCV000007523	SCV000594089	pathogenic	Cystic fibrosis	2016-08-26	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000007523	SCV000741228	pathogenic	Cystic fibrosis	2023-03-06	criteria provided, single submitter	clinical testing	The c.1521_1523delCTT (p.F508del) alteration is located in coding exon 11 of the CFTR gene, results from an in-frame CTT deletion at nucleotide positions 1521 to 1523. This results in the deletion of a phenylalanine residue at codon 508. Based on data from gnomAD, the c.1521_1523delCTT allele has an overall frequency of 0.717% (2027/282630) total alleles studied. The highest observed frequency was 1.238% (1598/129034) of European (non-Finnish) alleles. This mutation accounts for approximately 70% of cystic fibrosis chromosomes worldwide and is associated with elevated sweat chloride levels, lung disease, pancreatic insufficiency, and Pseudomonas infection (Sosnay, 2013). Disease expression is variable, even among individuals homozygous for p.F508del (Bronsveld, 2001). In vitro functional studies showed this mutation results in significantly reduced chloride conductance (Sosnay, 2013). It is a class II mutation which results in a misfolded CFTR protein that is subsequently degraded (Esposito, 2016). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.
Centre for Mendelian Genomics, University Medical Centre Ljubljana	RCV000626692	SCV000747395	likely pathogenic	Duodenal stenosis	2017-01-01	criteria provided, single submitter	clinical testing
Centre for Mendelian Genomics, University Medical Centre Ljubljana	RCV000626693	SCV000747396	pathogenic	Recurrent pancreatitis	2017-01-01	criteria provided, single submitter	clinical testing
Johns Hopkins Genomics, Johns Hopkins University	RCV000007523	SCV000864219	pathogenic	Cystic fibrosis	2019-01-15	criteria provided, single submitter	clinical testing
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	RCV000007523	SCV000883108	pathogenic	Cystic fibrosis	2019-06-04	criteria provided, single submitter	clinical testing
Mendelics	RCV000007523	SCV000886152	pathogenic	Cystic fibrosis	2018-11-05	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000058929	SCV000889288	pathogenic	not provided	2020-02-17	criteria provided, single submitter	clinical testing	The c.1521_1523del (p.Phe508del or Delta F508) pathogenic variant is an in-frame deletion of the phenylalanine amino acid at position p.508 of the CFTR protein. It is the most common cystic fibrosis pathogenic variant that accounts for approximately 70% of alleles in affected patients and causes a severe phenotype due to deleterious effects on CFTR protein maturation and function (PMID: 23857699 (2013), 23974870 (2013), 25148434 (2014), and 26581802 (2016)). Based on the available information, this variant is classified as pathogenic.
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University	RCV000007523	SCV000891676	pathogenic	Cystic fibrosis	2017-12-30	criteria provided, single submitter	clinical testing
Blueprint Genetics	RCV000058929	SCV000928113	pathogenic	not provided	2018-12-12	criteria provided, single submitter	clinical testing
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	RCV000007523	SCV001149705	pathogenic	Cystic fibrosis	2020-01-17	criteria provided, single submitter	clinical testing
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	RCV000007523	SCV001161676	pathogenic	Cystic fibrosis	2019-10-18	criteria provided, single submitter	clinical testing	A homozygous 3 base pair deletion in exon 11 of the CFTR gene that results in the in-frame deletion of Phenylalanine was detected. The observed variant c.1521_1523del (p.Phe508del) has a minor allele frequency of 0.4% and 0.68% in the 1000 Genomes and ExAC databases respectively. The observed variation has previously been identified in patients affected with cystic fibrosis and it lies in the ABC transporter domain of the CFTR protein (Riordan et al 1989). The in silico prediction of the variant is damaging by MutationTaster2. The reference codon is conserved across mammals. In summary, the variant meets our criteria to be classified as pathogenic.
Baylor Genetics	RCV001004459	SCV001163504	pathogenic	Cystic fibrosis; Congenital bilateral aplasia of vas deferens from CFTR mutation		criteria provided, single submitter	clinical testing
CFTR-France	RCV000007523	SCV001169465	pathogenic	Cystic fibrosis	2018-01-29	criteria provided, single submitter	curation
Myriad Genetics, Inc.	RCV000007523	SCV001193905	pathogenic	Cystic fibrosis	2019-10-18	criteria provided, single submitter	clinical testing	NM_000492.3(CFTR):c.1521_1523delCTT(aka F508del) is classified as pathogenic in the context of cystic fibrosis and is associated with the classic form of disease. Sources cited for classification include the following: PMID 23974870 and 15371902. Classification of NM_000492.3(CFTR):c.1521_1523delCTT(aka F508del) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV000007523	SCV001244997	pathogenic	Cystic fibrosis	2018-09-03	criteria provided, single submitter	clinical testing	A heterozygous inframe deletion variant, NM_000492.3(CFTR):c.1521_1523del, has been identified in exon 11 of 27 in the CFTR gene. The variant is predicted to result in an inframe deletion of a single amino acid at position 508 of the protein, NP_000483.3(CFTR):p.(Phe508del). The phenylalanine at this position has very high conservation (UCSC, 100 vertebrates), and is located in the ABC transporter 1 functional domain. This variant is present in the gnomAD database at a frequency of 0.7% (2027 heterozygotes, 1 homozygote), and has been previously reported multiple times in individuals with cystic fibrosis, being the most common causative variant in the CFTR gene (ClinVar; Egan, ME. et al. (2016)). Analysis of parental samples indicated this variant was maternally inherited. Based on information available at the time of curation, this variant has been classified as PATHOGENIC.
CeGaT Center for Human Genetics Tuebingen	RCV000058929	SCV001246813	pathogenic	not provided	2024-08-01	criteria provided, single submitter	clinical testing	CFTR: PM3:Very Strong, PS3:Moderate, PM2:Supporting, PM4:Supporting
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill	RCV000007523	SCV001251533	pathogenic	Cystic fibrosis		criteria provided, single submitter	research	The CFTR c.1521_1523delCTT (p.F508del) variant is the most common pathogenic CFTR variant (PMID: 20301428, 2233932).
Genomic Research Center, Shahid Beheshti University of Medical Sciences	RCV000058929	SCV001251746	pathogenic	not provided	2020-05-03	criteria provided, single submitter	clinical testing
Centre for Mendelian Genomics, University Medical Centre Ljubljana	RCV000119038	SCV001368335	pathogenic	Hereditary pancreatitis	2019-10-22	criteria provided, single submitter	clinical testing	This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM1,PM3,PM4.
Centogene AG - the Rare Disease Company	RCV000007523	SCV001424387	pathogenic	Cystic fibrosis		criteria provided, single submitter	clinical testing
Clinical Genetics and Genomics, Karolinska University Hospital	RCV000058929	SCV001450105	pathogenic	not provided	2014-07-29	criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000007523	SCV001527339	pathogenic	Cystic fibrosis	2024-01-07	criteria provided, single submitter	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000058929	SCV001713417	pathogenic	not provided	2023-05-31	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000007523	SCV001810348	pathogenic	Cystic fibrosis	2021-07-22	criteria provided, single submitter	clinical testing
Institute of Reproductive Genetics, University of Münster	RCV001642198	SCV001860325	pathogenic	Obstructive azoospermia	2021-08-23	criteria provided, single submitter	clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	RCV000058929	SCV002009133	pathogenic	not provided	2021-11-03	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000058929	SCV002019253	pathogenic	not provided	2023-02-15	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000058929	SCV002048630	pathogenic	not provided	2023-10-19	criteria provided, single submitter	clinical testing	The CFTR c.1521_1523del; p.Phe508del (F508del) variant is the most common pathogenic CFTR variant that has been reported in Caucasians (Sosnay 2013, CFTR2 database). This variant is considered to cause cystic fibrosis when identified with another pathogenic variant on the opposite chromosome. REFERENCES CFTR2 database: http://cftr2.org/ Sosnay P et al. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet. 2013;45(10):1160-7. PMID: 23974870.
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	RCV000007523	SCV002053836	pathogenic	Cystic fibrosis		criteria provided, single submitter	clinical testing
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	RCV000007523	SCV002061800	pathogenic	Cystic fibrosis	2021-12-30	criteria provided, single submitter	clinical testing	PS3, PP1, PM1, PM3, PM4
Institute of Human Genetics, University of Leipzig Medical Center	RCV000007523	SCV002072562	pathogenic	Cystic fibrosis	2024-09-09	criteria provided, single submitter	clinical testing	Criteria applied: PM3_VSTR,PS3,PM4; Identified as compund heterozygous with NM_000492.4:c.350G>A
DASA	RCV000007523	SCV002097285	pathogenic	Cystic fibrosis	2022-02-14	criteria provided, single submitter	clinical testing	Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 30030066; 27738188) - PS3. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID: 7105; PMID: 30089726; 29614238; 29668297; 29944384) - PS4. The p.(Phe508del) was detected in trans with a pathogenic variant (PMID: 30089726; 29614238) - PM3_very strong. Protein length variants as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants - PM4 and allele frequency is greater than expected for disorder - BS1. In summary, the currently available evidence indicates that the variant is pathogenic.
AiLife Diagnostics, AiLife Diagnostics	RCV000058929	SCV002502414	pathogenic	not provided	2022-03-30	criteria provided, single submitter	clinical testing
Molecular Genetics, Royal Melbourne Hospital	RCV000007523	SCV002503785	pathogenic	Cystic fibrosis	2023-03-30	criteria provided, single submitter	clinical testing	This sequence change is an inframe deletion of 3 bp predicted to cause the deletion of phenylalanine at position 508 of the CFTR protein, p.(Phe508del). The region deleted is highly conserved (100 vertebrates, UCSC) in a nonrepeat region, and is located in the ABC transporter domain. The variant is present in a large population cohort at a frequency of 0.7% (rs1297060838, 2,027/282,630 alleles, 1 homozygote in gnomAD v2.1). It is the most commonly reported pathogenic variant in CFTR, and is assigned a practice guideline pathogenic classification (ClinVar ID: 7105). It has been identified in a homozygous state and compound heterozygous with a second pathogenic allele in cystic fibrosis cases (PMID: 8092189, 1379413, 2570460). Additionally, a Cftr Phe508del/Phe508del mouse model lacks CFTR in the apical membrane, were chloride ion-impermeable, and displayed several abnormalities found in the human disease (PMID: 7560099). Based on the classification scheme RMH ACMG Guidelines v1.2.1, this variant is classified as PATHOGENIC. Following criteria are met: PM3_VeryStrong, PS3, PM4_Supporting.
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV000007523	SCV002507372	pathogenic	Cystic fibrosis	2019-10-11	criteria provided, single submitter	clinical testing
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	RCV002243627	SCV002512246	pathogenic	Cystic fibrosis; Hereditary pancreatitis	2022-02-01	criteria provided, single submitter	clinical testing	ACMG classification criteria: PS3 supporting, PS4 strong, PM3 very strong, PM3 strong, PM4 moderate, PP3 supporting
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	RCV002251888	SCV002523540	pathogenic	See cases	2019-05-03	criteria provided, single submitter	clinical testing	ACMG classification criteria: PS3, PM2, PM4, PP1, PP4, PP5
Sema4, Sema4	RCV000119038	SCV002529678	pathogenic	Hereditary pancreatitis	2021-05-12	criteria provided, single submitter	curation
Suma Genomics	RCV001004459	SCV002543782	pathogenic	Cystic fibrosis; Congenital bilateral aplasia of vas deferens from CFTR mutation		criteria provided, single submitter	clinical testing
Arcensus	RCV000007523	SCV002564582	pathogenic	Cystic fibrosis	2013-02-01	criteria provided, single submitter	clinical testing
MGZ Medical Genetics Center	RCV000007523	SCV002579737	pathogenic	Cystic fibrosis	2022-08-30	criteria provided, single submitter	clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	RCV000007523	SCV002759371	pathogenic	Cystic fibrosis	2022-12-08	criteria provided, single submitter	clinical testing
Genetics and Molecular Pathology, SA Pathology	RCV000007523	SCV002761398	pathogenic	Cystic fibrosis	2022-02-04	criteria provided, single submitter	clinical testing	This sequence change is an inframe deletion of 3 bp predicted to cause the deletion of phenylalanine at position 508 of the CFTR protein (p.Phe508del). The region deleted is highly conserved (100 vertebrates, UCSC) in a nonrepeat region, and is located in the ABC transporter domain. The variant is present in a large population cohort at a frequency of 0.7% (rs1297060838, 2,027/282,630 alleles, 1 homozygote in gnomAD v2.1). It is the most commonly reported pathongenic variant in CFTR, and is assigned a practice quideline pathogenic classification in ClinVar (ID: 7105). It has been identified in a homozygous state and compound heterozygous with a second pathogenic allele in cystic fibrosis cases (PMID: 8092189, 1379413, 2570460). Additionally, a Cftr Phe508del/Phe508del mouse model lack CFTR in the apical membrane, were chloride ion-impermeable, and displayed several abnormalities found in the human disease (PMID: 7560099). Based on the classification scheme RMH ACMG Guidelines v1.2.1, this variant is classified as PATHOGENIC. Following criteria are met: PM3_VeryStrong, PS3, PM4_Supporting.
Fulgent Genetics, Fulgent Genetics	RCV002490332	SCV002810876	pathogenic	Bronchiectasis with or without elevated sweat chloride 1; Cystic fibrosis; Hereditary pancreatitis; Congenital bilateral aplasia of vas deferens from CFTR mutation	2022-03-15	criteria provided, single submitter	clinical testing
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital	RCV000058929	SCV002818128	pathogenic	not provided	2022-12-17	criteria provided, single submitter	clinical testing
3billion	RCV000007523	SCV003841941	pathogenic	Cystic fibrosis	2023-02-23	criteria provided, single submitter	clinical testing	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.717%). Inframe deletion located in a nonrepeat region was predicted to change the length of the protein and disrupt normal protein function. The variant has been reported multiple times as an established pathogenic variant (ClinVar ID: VCV000007105 / PMID: 2475911 / 3billion dataset). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
Lifecell International Pvt. Ltd	RCV003227599	SCV003925476	pathogenic	Congenital bilateral aplasia of vas deferens from CFTR mutation		criteria provided, single submitter	clinical testing	A Heterozygous inframe indel variant c.1520_1522delTCT in Exon 11 of the CFTR gene that results in the amino acid substitution p.Phe508del was identified. The observed variant has a minor allele frequency of 0.00707/0.00800% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is medium, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic. (Variant ID 7105). This variant has been previously reported for Indian patients with congenital absence of the vas deferens by Sharma H et al., 2014. Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines.
Suma Genomics	RCV000007523	SCV004037030	pathogenic	Cystic fibrosis		criteria provided, single submitter	clinical testing
Human Genetics Bochum, Ruhr University Bochum	RCV000119038	SCV004042777	pathogenic	Hereditary pancreatitis	2023-02-28	criteria provided, single submitter	clinical testing	ACMG criteria used to clasify this variant:PS4, PM3_STR, PM4, PS3_SUP, PP1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	RCV000007523	SCV004046363	pathogenic	Cystic fibrosis		criteria provided, single submitter	clinical testing	This variant has been previously reported as the most common pathogenic variant in the CFTR gene, accounting for an estimated 30%-80% of pathogenic variants in cystic fibrosis (CF) (PMID: 20301428). Functional studies have demonstrated that this variant disrupts the normal function of the protein (PMID: 2475911). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.72% (2027/282630) and thus is presumed to be rare. Based on the available evidence, the c.1521_1523del (p.Phe508del) variant is classified as Pathogenic.
Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital	RCV000007523	SCV004100881	pathogenic	Cystic fibrosis	2023-11-06	criteria provided, single submitter	clinical testing	This is the most common CFTR pathogenic variant. The c.1521_1523delCTT variant results in an in-frame deletion of a single Phenylalanine residue at codon 508.
Molecular Genetics and NGS Laboratory, Hospital Fundacion Valle Del Lili	RCV002490332	SCV004101389	pathogenic	Bronchiectasis with or without elevated sweat chloride 1; Cystic fibrosis; Hereditary pancreatitis; Congenital bilateral aplasia of vas deferens from CFTR mutation	2023-11-07	criteria provided, single submitter	clinical testing
Neuberg Centre For Genomic Medicine, NCGM	RCV000007523	SCV004101520	pathogenic	Cystic fibrosis		criteria provided, single submitter	clinical testing	The observed inframe deletion c.1521_1523del (p.Phe508del) variant in the CFTR gene has been reported previously in both homozygous and compound heterozygous states in multiple individuals affected with cystic fibrosis (Sosnay et al., 2013; Terlizzi et al., 2021). Experimental studies have shown that this variant affects CFTR function (Zeiher et al. 1995). The p.Phe508del variant is reported with an allele frequency of 0.7% in the gnomAD Exomes. This variant has been submitted to the ClinVar database as Pathogenic (multiple submissions). This p.Phe508del causes deletion of amino acid Phenylalanine at position 508. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic.
Institute of Human Genetics, University Hospital of Duesseldorf	RCV003444054	SCV004171185	pathogenic	Bronchiectasis with or without elevated sweat chloride 1		criteria provided, single submitter	not provided
Neuberg Centre For Genomic Medicine, NCGM	RCV000119038	SCV004176446	pathogenic	Hereditary pancreatitis	2023-03-01	criteria provided, single submitter	clinical testing	The inframe deletion c.1521_1523del (p.Phe508del) variant in the CFTR gene has been reported previously in multiple individuals in homozygous/compound heterozygous state affected with Cystic fibrosis related disorders (Sosnay et al., 2013; Terlizzi et al., 2021). The p.Phe508del variant is the most frequent deletion that occurs in ~85% of Cystic fibrosis patients worldwide and is described to affect CFTR (class II) protein processing (Awatade et al. 2019). Experimental studies have shown that this variant affects CFTR function (Zeiher et al. 1995). The p.Phe508del variant is reported with an allele frequency of 0.7% in the gnomAD exomes database and is novel (not in any individuals) in the 1000 Genomes database. This variant has been reported to the ClinVar database as Pathogenic (multiple submissions). This p.Phe508del causes the deletion of the amino acid Phenylalanine at position 508. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics	RCV003444054	SCV004211619	pathogenic	Bronchiectasis with or without elevated sweat chloride 1	2024-03-30	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000058929	SCV004242533	pathogenic	not provided	2024-07-31	criteria provided, single submitter	clinical testing
Institute of Human Genetics, University of Leipzig Medical Center	RCV003444054	SCV004698102	pathogenic	Bronchiectasis with or without elevated sweat chloride 1	2024-02-15	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	RCV000007523	SCV004805438	pathogenic	Cystic fibrosis	2024-03-25	criteria provided, single submitter	research
Laboratory of Medical Genetics, National & Kapodistrian University of Athens	RCV000007523	SCV005051724	likely pathogenic	Cystic fibrosis	2024-02-01	criteria provided, single submitter	curation
Clinical Genetics Laboratory, Skane University Hospital Lund	RCV000058929	SCV005197698	pathogenic	not provided	2024-01-11	criteria provided, single submitter	clinical testing
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center	RCV000007523	SCV005397656	pathogenic	Cystic fibrosis	2024-01-24	criteria provided, single submitter	clinical testing	This sequence variant is an in-frame deletion of 3 nucleotides spanning positions 1521 through 1523 of the coding sequence of the CFTR gene that removes Phe508 of the CF transmembrane conductance regulator protein. This is a previously reported (ClinVar 7105), well characterized variant (PMID: 15371902) that is the most common cystic fibrosis-associated variant in the general population (PMID: 23974870). The variant is also known as deltaF508 and similar identifiers in the literature and public databases. This variant is present in 2976 of 403344 alleles (0.7378%) in the gnomAD population dataset. Experimental evidence shows that function of the variant protein is significantly inhibited (PMID: 2475911). Based upon the evidence, we consider this variant to be pathogenic. ACMG Criteria: PM4, PS3, PS4
OMIM	RCV000007523	SCV000027724	pathogenic	Cystic fibrosis	2015-05-17	no assertion criteria provided	literature only
OMIM	RCV000007524	SCV000053487	risk factor	Bronchiectasis with or without elevated sweat chloride 1, modifier of	2015-05-17	no assertion criteria provided	literature only
SNPedia	RCV000058929	SCV000090450	not provided	not provided		no assertion provided	not provided
GeneReviews	RCV000119038	SCV000153744	not provided	Hereditary pancreatitis		no assertion provided	literature only
Division of Human Genetics, Children's Hospital of Philadelphia	RCV000007523	SCV000536740	pathogenic	Cystic fibrosis	2016-06-10	no assertion criteria provided	research
GenomeConnect, ClinGen	RCV000007523	SCV000607274	not provided	Cystic fibrosis		no assertion provided	phenotyping only	Variant reported in multiple GenomeConnect participants by multiple clinical testing laboratories. Variant interpreted as Pathogenic by all laboratories and reported most recently on 10/28/2022 by ARUP Laboratories, INC, 06/29/2018 by Genetic Services Laboratory, University of Chicago, and 08/20/2015 by Mayo Clinic Genetic Testing Laboratories. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000058929	SCV001553614	pathogenic	not provided		no assertion criteria provided	clinical testing	The CFTR p.F508del variant is the most common variant known to cause cystic fibrosis (CF); this variant acounts for ~70% of CFTR variants and is present in approximately 85% of CF patients worldwide (Maiuri_2015_PMID:26046070). The variant was identified in dbSNP (ID: rs113993960) and ClinVar (classified as pathogenic by the American College of Medical Genetics and Genomics, Laboratory for Molecular Medicine and 20+ other laboratories). The variant was identified in control databases in 2027 of 282630 chromosomes (1 homozygous) at a frequency of 0.007172 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 1598 of 129034 chromosomes (freq: 0.01238), Other in 49 of 7214 chromosomes (freq: 0.006792), Ashkenazi Jewish in 58 of 10368 chromosomes (freq: 0.005594), Latino in 135 of 35426 chromosomes (freq: 0.003811), African in 65 of 24958 chromosomes (freq: 0.002604), European (Finnish) in 61 of 25074 chromosomes (freq: 0.002433) and South Asian in 61 of 30608 chromosomes (freq: 0.001993), but was not observed in the East Asian population. This variant is an in-frame deletion resulting in the removal of a phenylalanine (F) residue at codon 508; the deletion of p.F508 results in a misfolded mutant protein that is prematurely degraded before it reaches the plasma membrane (Maiuri_2015_PMID:26046070). In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.
GeneReviews	RCV000007523	SCV001622798	not provided	Cystic fibrosis		no assertion provided	literature only
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000058929	SCV001744105	pathogenic	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000058929	SCV001929598	pathogenic	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000058929	SCV002035293	pathogenic	not provided		no assertion criteria provided	clinical testing
Natera, Inc.	RCV001831519	SCV002080609	pathogenic	CFTR-related disorder	2017-03-17	no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV001831519	SCV002507456	pathogenic	CFTR-related disorder	2019-10-11	no assertion criteria provided	clinical testing
Genomics And Bioinformatics Analysis Resource, Columbia University	RCV000007523	SCV004024086	pathogenic	Cystic fibrosis		no assertion criteria provided	research
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas	RCV000007523	SCV004101106	pathogenic	Cystic fibrosis	2023-11-02	no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV001831519	SCV004105952	pathogenic	CFTR-related disorder	2024-09-26	no assertion criteria provided	clinical testing	The CFTR c.1521_1523delCTT variant is predicted to result in an in-frame deletion (p.Phe508del). This variant, frequently described as ΔF508, is known to disrupt protein function and is the most common cause of autosomal recessive cystic fibrosis (Riordan et al. 1989. PubMed ID: 2475911; Watson et al. 2004. PubMed ID: 15371902; Sosnay et al. 2013. PubMed ID: 23974870). This variant is reported in 1.2% of alleles in individuals of European (Non-Finnish) descent. In summary, we classify this variant as pathogenic.