ClinVar Miner

Submissions for variant NM_000071.3(CBS):c.573G>A (p.Thr191=) (rs73906420)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000179709 SCV000167561 benign not specified 2013-03-06 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.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000179709 SCV000232000 benign not specified 2015-02-19 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000179709 SCV000268835 benign not specified 2013-04-04 criteria provided, single submitter clinical testing Thr191Thr in exon 7 of CBS: This variant is not expected to have clinical signif icance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 0.7% (64/8600) of Euro pean American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs73906420).
Invitae RCV000755228 SCV000283387 benign Classic homocystinuria 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000254493 SCV000317357 likely benign Cardiovascular phenotype 2014-07-03 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000179709 SCV000602916 benign not specified 2018-11-13 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000755228 SCV001298057 benign Classic homocystinuria 2017-06-26 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.
Integrated Genetics/Laboratory Corporation of America RCV000179709 SCV001338212 benign not specified 2020-02-24 criteria provided, single submitter clinical testing Variant summary: CBS c.573G>A alters a non-conserved nucleotide resulting in a synonymous change. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0059 in 248930 control chromosomes in the gnomAD database, including 12 homozygotes. The observed variant frequency is approximately 2 fold of the estimated maximal expected allele frequency for a pathogenic variant in CBS causing Homocystinuria phenotype (0.003), strongly suggesting that the variant is benign. Four ClinVar submitters (evaluation after 2014) cite the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.

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