ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.3403-14A>G

gnomAD frequency: 0.00007  dbSNP: rs941737393
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV001180818 SCV001345842 likely benign Hereditary cancer-predisposing syndrome 2016-02-26 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001356014 SCV001551063 likely benign Carcinoma of colon no assertion criteria provided clinical testing The ATM c.3403-14A>G variant was not identified in the literature nor was it identified in the Cosmic, MutDB, LOVD 3.0, dbSNP, ClinVar, or Clinvitae. The variant was identified in control databases in 1 of 6652 chromosomes at a frequency of 0.0002 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). It was observed in the European (Non-Finnish) population in 1 of 2836 chromosomes (freq: 0.0004); it was not observed in the East Asian, South Asian, African, Other, Latino, Ashkenazi Jewish, or Finnish populations. Another similar variant (c.3403-14_3403-13insG) was observed in one individual with ovarian cancer from our laboratory with a co-occurring BRCA1 pathogenic variant, increasing the likelihood a substitution at this position does not have clinical significance. The c.3403-14A>G variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information we lean towards a more benign role for this variant. This variant is classified as likely benign.

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