ClinVar Miner

Submissions for variant NM_000260.4(MYO7A):c.471-1G>A

gnomAD frequency: 0.00001  dbSNP: rs548172627
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000673992 SCV000799260 likely pathogenic Autosomal recessive nonsyndromic hearing loss 2; Usher syndrome type 1 2018-04-06 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001868273 SCV002280827 likely pathogenic not provided 2023-10-05 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 5 of the MYO7A 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 MYO7A are known to be pathogenic (PMID: 8900236, 25404053). This variant is present in population databases (rs548172627, gnomAD 0.003%). Disruption of this splice site has been observed in individual(s) with Usher syndrome type 1 (PMID: 18181211). ClinVar contains an entry for this variant (Variation ID: 557808). 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.
Genomics, Clalit Research Institute, Clalit Health Care RCV004554819 SCV005043785 pathogenic Usher syndrome type 1 criteria provided, single submitter clinical testing Inheritance: The variant was identified in the Homozygous state in the sample (pm3_support. Frequency: The variant is rare, observed in 1 alleles out of 249,202 (0%) in the gnomAD reference population dataset. Frequency among cases: This variant has been observed in individuals with Usher syndrome type 1 (PMID: 18181211,PMID:25404053, etc.) (ps4). Variant type: Canonical splice site variant in a gene where loss of function is a known mechanism of disease (pvs1_strong) Clinical evidence: This variant has previously been described in ClinVar (VCV557808) with the following classifications: LP (2). Gene coverage: 100% of the MYO7A target region is covered with at least 10x.
Juno Genomics, Hangzhou Juno Genomics, Inc RCV004796273 SCV005415893 pathogenic Autosomal dominant nonsyndromic hearing loss 11; Autosomal recessive nonsyndromic hearing loss 2; Usher syndrome type 1 criteria provided, single submitter clinical testing PVS1+PM2_Supporting+PM3_Supporting

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