ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.6082del (p.Gln2028fs)

dbSNP: rs1565499093
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Department of Molecular Diagnostics, Institute of Oncology Ljubljana RCV000755037 SCV000882857 likely pathogenic Hereditary cancer-predisposing syndrome 2018-10-24 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001231387 SCV001403907 pathogenic Ataxia-telangiectasia syndrome 2022-10-31 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 617781). This variant has not been reported in the literature in individuals affected with ATM-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln2028Asnfs*19) in the ATM gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATM are known to be pathogenic (PMID: 23807571, 25614872).
Ambry Genetics RCV000755037 SCV002657980 pathogenic Hereditary cancer-predisposing syndrome 2021-12-27 criteria provided, single submitter clinical testing The c.6082delC pathogenic mutation, located in coding exon 40 of the ATM gene, results from a deletion of one nucleotide at nucleotide position 6082, causing a translational frameshift with a predicted alternate stop codon (p.Q2028Nfs*19). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV002467452 SCV002762778 pathogenic Familial cancer of breast 2022-12-09 criteria provided, single submitter research PVS1, PM2_SUP, PM3_SUP
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV001231387 SCV004228465 likely pathogenic Ataxia-telangiectasia syndrome 2023-12-30 criteria provided, single submitter clinical testing A homozygous single base pair deletion in exon 41 of the ATM gene that results in a frameshift and premature truncation of the protein 19 amino acids downstream to codon 2028 (p.Gln2028AsnfsTer19) was detected. This variant has not been reported in the 1000 genomes, gnomAD (v3.1), gnomdAD (v2.1) and topmed databases. The reference region is conserved across species. In summary, the variant meets our criteria to be classified as likely pathogenic.
BRCAlab, Lund University RCV002467452 SCV002588944 pathogenic Familial cancer of breast 2022-08-26 no assertion criteria provided clinical testing

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