Submissions for variant NM_005359.6(SMAD4):c.424+5G>A

gnomAD frequency: 0.00010  dbSNP: rs200772603

Total submissions: 21

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000656977	SCV000149792	uncertain significance	not provided	2025-03-11	criteria provided, single submitter	clinical testing	In silico analysis supports that this variant does not alter splicing; however, published functional studies demonstrate evidence of aberrant splicing (Shiraishi Y et al. Systematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data. bioRxiv. October 7, 2021); Observed in individuals with Lynch syndrome-associated cancer, familial gastric cancer, pancreatic cancer, breast cancer, or polyps, but has not been published in individuals with connective tissue disorders to our knowledge (PMID: 25186627, 27146957, 28726808, 30426508, 32066632, 34326862, 35534704); This variant is associated with the following publications: (PMID: 32066632, 25980754, 28873162, 31159747, 27146957, Shiraishi2021, 25186627, 28726808, 30426508, 35534704, 34326862)
Ambry Genetics	RCV002311002	SCV000186740	likely benign	Familial thoracic aortic aneurysm and aortic dissection; Hereditary cancer-predisposing syndrome	2019-05-24	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Labcorp Genetics (formerly Invitae), Labcorp	RCV002228348	SCV000259352	likely benign	Juvenile polyposis syndrome	2025-01-28	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000346296	SCV000409087	benign	Myhre syndrome	2018-01-13	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Laboratory Services, Illumina	RCV000204731	SCV000409088	likely benign	Generalized juvenile polyposis/juvenile polyposis coli	2018-01-13	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Illumina Laboratory Services, Illumina	RCV000306889	SCV000409089	uncertain significance	Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome	2018-01-13	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000656977	SCV000602194	benign	not provided	2023-04-19	criteria provided, single submitter	clinical testing	The frequency of this variant in the general population, 0.00037 (47/128762 chromosomes in European (Non-Finnish) subpopulation, http://gnomad.broadinstitute.org), is higher than would generally be expected for pathogenic variants in this gene. In the published literature, the variant has been reported in individuals with breast and/or ovarian cancer (PMIDs: 31159747 (2019), 30426508 (2018), and 25186627 (2015)), pancreatic cancer (PMID: 28726808 (2018)), gastric cancer (PMID: 32066632 (2021)), colon cancer (PMID: 25980754 (2015)), and hamartomatous polyposis syndrome (PMID: 2714957 (2016)). Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper SMAD4 mRNA splicing . Based on the available information, we are unable to determine the clinical significance of this variant.
Color Diagnostics, LLC DBA Color Health	RCV000115883	SCV000686539	likely benign	Hereditary cancer-predisposing syndrome	2020-11-17	criteria provided, single submitter	clinical testing
Counsyl	RCV000204731	SCV000786540	likely benign	Generalized juvenile polyposis/juvenile polyposis coli	2018-05-23	criteria provided, single submitter	clinical testing
GeneKor MSA	RCV000115883	SCV000822202	uncertain significance	Hereditary cancer-predisposing syndrome	2018-08-01	criteria provided, single submitter	clinical testing
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV000770696	SCV000902173	uncertain significance	Familial thoracic aortic aneurysm and aortic dissection	2016-11-25	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000213004	SCV000918223	likely benign	not specified	2024-05-03	criteria provided, single submitter	clinical testing	Variant summary: SMAD4 c.424+5G>A alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant weakens a 5' donor site. One predict the variant abolishes a 5 splicing donor site. One predict the variant no significant impact on splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00022 in 250792 control chromosomes. The observed variant frequency is approximately 110 fold of the estimated maximal expected allele frequency for a pathogenic variant in SMAD4 causing Juvenile Polyposis Syndrome phenotype (2e-06), strongly suggesting that the variant is benign. c.424+5G>A has been reported in the literature in individuals affected with cancer including colorectal cancer, hereditary breast and ovarian cancer, pancreatic ductal adenocarcinoma and familial intestinal gastric cancer (e.g. Tung_2015, Yurgelun_2015, Mandelker_2017, Chaffee_2018, Schubert_2019, Tsaousis_2019, Carvalho_2021). These reports do not provide unequivocal conclusions about association of the variant with Juvenile Polyposis Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 25980754, 25186627, 27146957, 28873162, 28726808, 30426508, 31159747, 32066632). ClinVar contains an entry for this variant (Variation ID: 127950). Based on the evidence outlined above, the variant was classified as likely benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000656977	SCV001157713	uncertain significance	not provided	2021-01-31	criteria provided, single submitter	clinical testing	The SMAD4 c.424+5G>A variant (rs200772603) is reported in the literature in an individual with suspected Lynch syndrome (Yurgelun 2015) and another individual referred for hereditary cancer testing (Tsaousis 2019). This variant is found in the non-Finnish European population with an overall allele frequency of 0.04% (47/128762 alleles) in the Genome Aggregation Database. This is an intronic variant in a highly conserved nucleotide, and computational analyses (Alamut v.2.11) predict that this variant may impact splicing by weakening the nearby canonical donor splice site. However, given the lack of clinical and functional data, the significance of the c.424+5G>A variant is uncertain at this time. References: Tsaousis et al. Analysis of hereditary cancer syndromes by using a panel of genes: novel and multiple pathogenic mutations. BMC Cancer. 2019 Jun 3;19(1):535. Yurgelun MB et al. Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome. Gastroenterology. 2015 Sep;149(3):604-13.e20.
Genetic Services Laboratory, University of Chicago	RCV000213004	SCV002068341	likely benign	not specified	2021-08-31	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV000115883	SCV002538323	likely benign	Hereditary cancer-predisposing syndrome	2020-11-12	criteria provided, single submitter	curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000213004	SCV002551307	uncertain significance	not specified	2025-03-04	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV000306889	SCV004017793	likely benign	Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome	2023-04-10	criteria provided, single submitter	clinical testing	This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing. Homozygosity has been confirmed in one or more individuals. As homozygosity for pathogenic variants in this gene is generally assumed to result in embryonic lethality, this variant is unlikely to be pathogenic.
CeGaT Center for Human Genetics Tuebingen	RCV000656977	SCV004701678	likely benign	not provided	2025-01-01	criteria provided, single submitter	clinical testing	SMAD4: BP4, BS2
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000656977	SCV001956576	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000656977	SCV001966476	likely benign	not provided		no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV004745191	SCV005361066	likely benign	SMAD4-related disorder	2024-06-10	no assertion criteria provided	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).