ClinVar Miner

Submissions for variant NM_000038.6(APC):c.2608C>T (p.Pro870Ser)

gnomAD frequency: 0.00917  dbSNP: rs33974176
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Total submissions: 24
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000035068 SCV000058708 likely benign not specified 2011-03-29 criteria provided, single submitter clinical testing Pro870Ser in exon 15 of APC: The Pro870Ser variant has been reported in the lite rature in two individuals with multiple sporadic colorectal adenomas and was abs ent from 1938 age, sex, and race-matched control chromosomes (Azzopardi 2008). T his variant has been reported in dbSNP with a frequency of about 2% (rs 33974176 ). Proline (Pro) at amino acid position 870 is not highly conserved in mammals o r lower species, with mouse carrying an alanine and both chicken and frog carryi ng a serine (this variant). Collectively this data suggests a more likely benign role for this variant.
Eurofins Ntd Llc (ga) RCV000035068 SCV000109816 benign not specified 2013-10-01 criteria provided, single submitter clinical testing
GeneDx RCV000035068 SCV000167002 benign not specified 2013-12-31 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Ambry Genetics RCV000157720 SCV000212890 benign Hereditary cancer-predisposing syndrome 2014-11-19 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: 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.
Invitae RCV003534313 SCV000261825 benign Familial adenomatous polyposis 1 2024-02-01 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000400276 SCV000451999 likely benign APC-Associated Polyposis Disorders 2018-02-16 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Counsyl RCV000204735 SCV000488432 benign Familial adenomatous polyposis 1 2016-03-28 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000034382 SCV000610978 likely benign not provided 2017-05-22 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000157720 SCV000681539 benign Hereditary cancer-predisposing syndrome 2015-03-19 criteria provided, single submitter clinical testing
Center for Human Genetics, Inc, Center for Human Genetics, Inc RCV000659276 SCV000781074 likely benign Familial multiple polyposis syndrome 2016-11-01 criteria provided, single submitter clinical testing
Preventiongenetics, part of Exact Sciences RCV000035068 SCV000805384 benign not specified 2016-11-09 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000034382 SCV000883403 benign not provided 2017-08-20 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000157720 SCV002538560 benign Hereditary cancer-predisposing syndrome 2020-07-31 criteria provided, single submitter curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV000035068 SCV002550603 benign not specified 2023-08-15 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV000204735 SCV004017683 benign Familial adenomatous polyposis 1 2023-07-07 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000034382 SCV004159219 benign not provided 2023-09-01 criteria provided, single submitter clinical testing APC: BP4, BS1, BS2
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. RCV000157720 SCV004228003 benign Hereditary cancer-predisposing syndrome 2023-11-06 criteria provided, single submitter clinical testing
Biesecker Lab/Clinical Genomics Section, National Institutes of Health RCV000034382 SCV000043116 no known pathogenicity not provided 2012-07-13 no assertion criteria provided research Converted during submission to Benign.
ITMI RCV000035068 SCV000084154 not provided not specified 2013-09-19 no assertion provided reference population
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001353782 SCV000591113 benign Carcinoma of colon no assertion criteria provided clinical testing The APC p.Pro870Ser variant was identified by Azzopardi (2008) in 2 of 1382 proband chromosomes from individuals with colorectal adenomas and was absent in the 1938 control chromosomes evaluated from this study. The variant was also identified in the HGMD and LOVD databases, and in dbSNP (ID: rs33974176) with an average heterozygosity of 0.024+/-0.106. This variant occurs at a frequency of greater than 1% in some populations of origin, including the 1000 Genomes Project (1.2%) and NHLBI Exome Sequencing Project (3.2% in African American alleles), and is therefore classified as a polymorphism. The p.Pro870 residue is not conserved across mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD) do not suggest a high likelihood of impact of the variant to the protein. In addition, our laboratory has identified this variant co-occurring with a pathogenic APC variant in a patient sample, further increasing the likelihood that the p.Pro870Ser variant does not have clinical significance. In summary, based on the above information, this variant meets our laboratory's criteria to be classified as benign.
True Health Diagnostics RCV000157720 SCV000787833 likely benign Hereditary cancer-predisposing syndrome 2018-01-12 no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000035068 SCV001800515 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000035068 SCV001808904 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000035068 SCV001964363 benign not specified no assertion criteria provided clinical testing

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