ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.6096-3T>C

gnomAD frequency: 0.00001  dbSNP: rs748380897
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000572845 SCV000672625 likely benign Hereditary cancer-predisposing syndrome 2022-06-23 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000628094 SCV000748984 likely benign Ataxia-telangiectasia syndrome 2025-01-22 criteria provided, single submitter clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV003237939 SCV002010798 uncertain significance not provided 2021-11-03 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV004592763 SCV005085143 likely benign Familial cancer of breast 2024-06-03 criteria provided, single submitter clinical testing This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing.
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001355568 SCV001550491 uncertain significance Familial ovarian cancer no assertion criteria provided clinical testing The ATM c.6096-3T>C variant was not identified in the literature nor was it identified in the COGR, Cosmic, or LOVD 3.0 databases. The variant was identified in dbSNP (ID: rs748380897) as "With Uncertain significance allele" and ClinVar (classified as uncertain significance by Invitae and Ambry Genetics). The variant was identified in control databases in 2 of 246130 chromosomes at a frequency of 0.000008 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European in 1 of 111648 chromosomes (freq: 0.000009) and East Asian in 1 of 17212 chromosomes (freq: 0.00006); it was not observed in the African, Other, Latino, Ashkenazi Jewish, Finnish, or South Asian populations. The c.6096-3T>C variant is located in the 3' splice region and does not affect the invariant -1 and -2 positions, although positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. However, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.
Natera, Inc. RCV000628094 SCV002078053 uncertain significance Ataxia-telangiectasia syndrome 2021-05-26 no assertion criteria provided clinical testing

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