ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.7789-3T>G (rs864622185)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000206828 SCV000259612 pathogenic Ataxia-telangiectasia syndrome 2018-11-16 criteria provided, single submitter clinical testing This sequence change falls in intron 52 of the ATM gene. It does not directly change the encoded amino acid sequence of the ATM protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has been observed as homozygous or on the opposite chromosome (in trans) from other pathogenic variants in several individuals affected with ataxia-telangiectasia (PMID: 8808599, 21965147, 17124347, 12815592). This finding is consistent with autosomal recessive inheritance, and suggests that this variant contributes to disease. ClinVar contains an entry for this variant (Variation ID: 219629). Nucleotide substitutions within the consensus splice site are relatively common causes of aberrant splicing (PMID: 17576681, 9536098). Experimental studies have shown that this variant leads to skipping of exon 53, generating a frameshift at codon 2597 (PMID: 8808599, 21965147). This creates a premature translational stop signal (p.Asp2597Lysfs*3) and is expected to result in an absent or disrupted protein product. For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics RCV000562166 SCV000665478 likely pathogenic Hereditary cancer-predisposing syndrome 2019-04-30 criteria provided, single submitter clinical testing Detected in individual satisfying established diagnostic critera for classic disease without a clear mutation;In silico models in agreement (deleterious) and/or completely conserved position in appropriate species;Functionally-validated splicing mutation
Color RCV000562166 SCV000682436 pathogenic Hereditary cancer-predisposing syndrome 2015-11-30 criteria provided, single submitter clinical testing
Counsyl RCV000206828 SCV000791081 likely pathogenic Ataxia-telangiectasia syndrome 2017-04-21 criteria provided, single submitter clinical testing
Mendelics RCV000206828 SCV000838597 pathogenic Ataxia-telangiectasia syndrome 2018-07-02 criteria provided, single submitter clinical testing

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