ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.5319+1G>A

dbSNP: rs876660175
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000214126 SCV000277382 likely pathogenic Hereditary cancer-predisposing syndrome 2015-07-23 criteria provided, single submitter clinical testing The c.5319+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 34 of the ATM gene. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6498 samples (12996 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.002% (greater than66000alleles tested) in our clinical cohort.This nucleotide position is highly conserved in available vertebrate species. Alterations that disrupt the canonical splice donor site are typically deleterious in nature (ACMG Recommendations for Standards for Interpretation and Reporting of Sequence Variations. Revision 2007. Genet Med. 2008;10:294). As such, the c.5319+1G>A variant is classified as likely pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV002519724 SCV003243746 likely pathogenic Ataxia-telangiectasia syndrome 2022-12-06 criteria provided, single submitter clinical testing Disruption of this splice site has been observed in individual(s) with breast and/or ovarian cancer (PMID: 30982232). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 233078). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 35 of the ATM gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ATM are known to be pathogenic (PMID: 23807571, 25614872).

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