ClinVar Miner

Submissions for variant NM_000441.2(SLC26A4):c.1615-2A>G

gnomAD frequency: 0.00001  dbSNP: rs758823761
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001335321 SCV001528448 pathogenic Autosomal recessive nonsyndromic hearing loss 4 2018-01-18 criteria provided, single submitter clinical testing This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been previously reported in patients with Pendred syndrome [PMID 21416585, 24224479]
Invitae RCV001389807 SCV001591288 pathogenic not provided 2023-10-15 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 14 of the SLC26A4 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 SLC26A4 are known to be pathogenic (PMID: 16283880, 25394566, 26252218, 26445815). This variant is present in population databases (rs758823761, gnomAD 0.0009%). Disruption of this splice site has been observed in individuals with Pendred syndrome (PMID: 21416585, 24224479). It has also been observed to segregate with disease in related individuals. This variant is also known as IVS14-2A>G. ClinVar contains an entry for this variant (Variation ID: 1033029). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001389807 SCV001780309 pathogenic not provided 2021-06-03 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in an in-frame deletion of a critical region; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 25394566, 21704276, 21416585, 24224479, 25525159)
Otorhinolaryngology Lab - LIM32, University of Sao Paulo School of Medicine Clinics Hospital RCV001335321 SCV001792215 likely pathogenic Autosomal recessive nonsyndromic hearing loss 4 criteria provided, single submitter research in compound heterozygosis with the c.481T>A variant in a subject with bilateral non-syndromic sensorineural prelingual hearing loss (familial)
Genome-Nilou Lab RCV001335321 SCV002026953 pathogenic Autosomal recessive nonsyndromic hearing loss 4 2021-09-05 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV001389807 SCV004225733 pathogenic not provided 2022-05-10 criteria provided, single submitter clinical testing PP1, PP3, PM2, PM3_strong, PVS1_moderate
Natera, Inc. RCV001830394 SCV002080003 pathogenic Pendred syndrome 2020-07-22 no assertion criteria provided clinical testing

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