ClinVar Miner

Submissions for variant NM_000489.6(ATRX):c.3158C>A (p.Thr1053Asn)

gnomAD frequency: 0.00007  dbSNP: rs151273832
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001226215 SCV001398520 benign Alpha thalassemia-X-linked intellectual disability syndrome 2023-11-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003479298 SCV004223643 likely benign not specified 2023-11-10 criteria provided, single submitter clinical testing Variant summary: ATRX c.3158C>A (p.Thr1053Asn) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 2.2e-05 in 181978 control chromosomes with 1 hemizygote, predominantly at a frequency of 0.00031 within the African or African-American subpopulation in the gnomAD database. To our knowledge, no occurrence of c.3158C>A in individuals affected with ATR-X Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as benign. Based on the evidence outlined above, the variant was classified as likely benign.

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