ClinVar Miner

Submissions for variant NM_000038.6(APC):c.1743+1G>T

dbSNP: rs761458613
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000217961 SCV000277037 likely pathogenic Hereditary cancer-predisposing syndrome 2017-12-04 criteria provided, single submitter clinical testing The c.1743+1G>T intronic variant results from a G to T substitution one nucleotide after N/A of the APC gene. This variant was reported in one French patient with diagnosed with FAP (Lagarde A et al J. Med. Genet. 2010 Oct; 47(10):721-2). Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native splice donor site; however, direct evidence is unavailable. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.
Invitae RCV003743662 SCV000647196 likely pathogenic Familial adenomatous polyposis 1 2023-12-28 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 14 of the APC 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 APC are known to be pathogenic (PMID: 17963004, 20685668). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with familial adenomatous polyposis (PMID: 20685668). ClinVar contains an entry for this variant (Variation ID: 232800). 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 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.
Sema4, Sema4 RCV000217961 SCV002529640 likely pathogenic Hereditary cancer-predisposing syndrome 2022-02-11 criteria provided, single submitter curation
Myriad Genetics, Inc. RCV003337258 SCV004045529 likely pathogenic Familial adenomatous polyposis 1 2023-05-03 criteria provided, single submitter clinical testing This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.

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