ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.3369G>A (p.Pro1123=)

gnomAD frequency: 0.00362  dbSNP: rs61733679
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000078050 SCV000109888 benign not specified 2013-02-26 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000302449 SCV000384657 uncertain significance Wilson disease 2018-01-12 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000302449 SCV000626839 benign Wilson disease 2024-01-31 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000588949 SCV000694445 likely benign not provided 2016-06-15 criteria provided, single submitter clinical testing Variant summary: The ATP7B c.3369G>A (p.Pro1123Pro) variant causes a synonymous change involving a non-conserved nucleotide with 4/5 splice prediction tools predicting no significant impact on splicing, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 135/120756 (1/894), predominantly in the African cohort, 118/9800 (1/83), which exceeds the estimated maximal expected allele frequency for a pathogenic ATP7B variant of 1/1851. Therefore, suggesting the variant of interest is a common polymorphism found in population(s) of African origin. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. A reputable clinical laboratory cites the variant as "benign." Therefore, taking all available lines of evidence into consideration, the variant of interest has been classified as likely benign until additional information becomes available.
GeneDx RCV000588949 SCV000726134 likely benign not provided 2021-06-24 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000302449 SCV000883433 benign Wilson disease 2022-03-08 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000302449 SCV001977131 likely benign Wilson disease 2021-08-10 criteria provided, single submitter clinical testing
Ambry Genetics RCV002453394 SCV002615508 likely benign Inborn genetic diseases 2022-08-10 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.
All of Us Research Program, National Institutes of Health RCV000302449 SCV004845370 likely benign Wilson disease 2024-02-05 criteria provided, single submitter clinical testing
Natera, Inc. RCV000302449 SCV002086814 likely benign Wilson disease 2019-10-23 no assertion criteria provided clinical testing

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