ClinVar Miner

Submissions for variant NM_000091.4(COL4A3):c.346C>A (p.Pro116Thr) (rs115324397)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000248076 SCV000302074 benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000248076 SCV000730618 likely benign not specified 2017-11-17 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.
Athena Diagnostics Inc RCV000710817 SCV000841122 benign not provided 2019-07-17 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000248076 SCV000919244 likely benign not specified 2018-01-08 criteria provided, single submitter clinical testing Variant summary: The COL4A3 c.346C>A (p.Pro116Thr) variant involves the alteration of a conserved nucleotide located in the Collagen triple helix repeat domain of the protein (InterPro). 4/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 1348/277088 control chromosomes (7 homozygotes), predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.008757 (1109/126648). This frequency is about 4 times the estimated maximal expected allele frequency of a pathogenic COL4A3 variant (0.0020412), suggesting this is likely a benign polymorphism found primarily in the populations of European (Non-Finnish) origin. This variant has been reported in multiple affected individuals without stong evidence for causality. In addition, one other clinical diagnostic laboratory classified this variant as benign. Taken together, this variant is classified as likely benign.
Invitae RCV000710817 SCV001099364 benign not provided 2020-12-06 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001138282 SCV001298323 benign Alport syndrome 2017-04-27 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 rule this variant out of causing disease. Therefore, this variant is classified as benign.
Cavalleri Lab, Royal College of Surgeons in Ireland RCV001171336 SCV001328283 likely benign Chronic kidney disease 2020-05-28 criteria provided, single submitter research PP3, BP6, BS1
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000248076 SCV001652983 benign not specified 2021-02-17 criteria provided, single submitter clinical testing The p.Pro116Thr variant in COL4A3 is classified as benign because it has been identified in 0.9% (1119/128642) of European chromosomes by gnomAD ( This variant has also been reported as benign and likely benign in ClinVar (Variation ID 254994). ACMG/AMP criteria applied: BA1, BP4.

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