ClinVar Miner

Submissions for variant NM_033100.4(CDHR1):c.55+1G>A

gnomAD frequency: 0.00036  dbSNP: rs547198427
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Blueprint Genetics RCV001073921 SCV001239486 likely pathogenic Retinal dystrophy 2018-06-19 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001377811 SCV001575236 likely pathogenic not provided 2025-02-02 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 1 of the CDHR1 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 CDHR1 are known to be pathogenic (PMID: 23044944, 23591405, 26103963, 26261414). This variant is present in population databases (rs547198427, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with CDHR1-related conditions. ClinVar contains an entry for this variant (Variation ID: 866140). 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.
PreventionGenetics, part of Exact Sciences RCV003393836 SCV004120226 likely pathogenic CDHR1-related disorder 2023-05-03 criteria provided, single submitter clinical testing The CDHR1 c.55+1G>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.13% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/10-85954572-G-A). Variants that disrupt the consensus splice donor site in CDHR1 are expected to be pathogenic. Therefore we interpret c.55+1G>A as likely pathogenic.

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