ClinVar Miner

Submissions for variant NM_001184.4(ATR):c.3945+2dup

gnomAD frequency: 0.00004  dbSNP: rs537031994
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000276456 SCV000441434 uncertain significance Seckel syndrome 2016-06-14 criteria provided, single submitter clinical testing
GeneDx RCV000485710 SCV000570959 uncertain significance not specified 2016-07-08 criteria provided, single submitter clinical testing The c.3945+2dupT variant in the ATR gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This splice site variant destroys the canonical splice donor site in intron 21, resulting in an in-frame protein product with an abnormal message. However, in the absence of RNA/functional studies, the actual effect of c.3945+2dupT is unknown. The c.3945+2dupT variant variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret c.3945+2dupT variant as a variant of uncertain significance.
Invitae RCV001861210 SCV002124039 uncertain significance not provided 2023-12-27 criteria provided, single submitter clinical testing This sequence change falls in intron 21 of the ATR gene. It does not directly change the encoded amino acid sequence of the ATR protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs537031994, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with ATR-related conditions. ClinVar contains an entry for this variant (Variation ID: 343608). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Genome-Nilou Lab RCV003126684 SCV003801620 uncertain significance Seckel syndrome 1 2023-02-08 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003126685 SCV003801621 uncertain significance Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome 2023-02-08 criteria provided, single submitter clinical testing

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