ClinVar Miner

Submissions for variant NM_002691.4(POLD1):c.1017G>T (p.Ser339=)

gnomAD frequency: 0.00013  dbSNP: rs373404887
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001083805 SCV000287497 likely benign Colorectal cancer, susceptibility to, 10 2024-01-27 criteria provided, single submitter clinical testing
GeneDx RCV000759208 SCV000527422 likely benign not provided 2020-12-14 criteria provided, single submitter clinical testing
Ambry Genetics RCV000573985 SCV000670939 likely benign Hereditary cancer-predisposing syndrome 2015-07-08 criteria provided, single submitter clinical testing This alteration is classified as likely 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759208 SCV000888425 benign not provided 2023-07-17 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV001818597 SCV002071295 likely benign not specified 2020-11-13 criteria provided, single submitter clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV001818597 SCV002551899 likely benign not specified 2023-08-15 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003955327 SCV004771884 likely benign POLD1-related condition 2019-07-17 criteria provided, single submitter 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).
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001355082 SCV001549854 likely benign Bile duct cancer no assertion criteria provided clinical testing The POLD1 p.Ser339= variant was not identified in the literature. The variant was identified in dbSNP (ID: rs373404887) as "With Likely benign allele" and ClinVar (classified as likely benign by Invitae, GeneDx and Ambry Genetics). The variant was identified in control databases in 16 of 197712 chromosomes at a frequency of 0.00008 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 1 of 17944 chromosomes (freq: 0.00006) and European in 15 of 82470 chromosomes (freq: 0.0002), while the variant was not observed in the Other, Latino, Ashkenazi Jewish, East Asian, Finnish, or South Asian populations. The p.Ser339= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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