ClinVar Miner

Submissions for variant NM_015662.3(IFT172):c.402+2T>G

gnomAD frequency: 0.00002  dbSNP: rs774548930
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002006167 SCV002273077 likely pathogenic Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71 2025-01-13 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 5 of the IFT172 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 IFT172 are known to be pathogenic (PMID: 24140113). This variant is present in population databases (rs774548930, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with IFT172-related conditions. ClinVar contains an entry for this variant (Variation ID: 1487038). 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.
Fulgent Genetics, Fulgent Genetics RCV002497968 SCV002797346 likely pathogenic Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71; Bardet-Biedl syndrome 20 2022-04-14 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004738483 SCV005341493 likely pathogenic IFT172-related disorder 2024-05-14 no assertion criteria provided clinical testing The IFT172 c.402+2T>G 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 0.020% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. Variants that disrupt the consensus splice donor site in IFT172 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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