ClinVar Miner

Submissions for variant NM_000441.2(SLC26A4):c.1149+3A>G

gnomAD frequency: 0.00002  dbSNP: rs111033314
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001574741 SCV001801611 pathogenic not provided 2019-01-03 criteria provided, single submitter clinical testing Non-canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; functional studies confirm variant destroys the splice donor site of intron 9 and causes skipping of exon 9 (Park et al., 2005); This variant is associated with the following publications: (PMID: 31387071, 31033086, 15679828, 28964290, 24007330, 25488846, 25525159, 23469187)
Fulgent Genetics, Fulgent Genetics RCV002477083 SCV002790737 pathogenic Autosomal recessive nonsyndromic hearing loss 4; Pendred syndrome 2022-03-09 criteria provided, single submitter clinical testing
3billion RCV003152674 SCV003841766 pathogenic Autosomal recessive nonsyndromic hearing loss 4 2023-02-23 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.002%). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 4 similarly affected unrelated individuals (PMID: 15679828, 31387071). The variant has been reported to be associated with SLC26A4 related disorder (ClinVar ID: VCV000043493). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
Baylor Genetics RCV003152674 SCV004201943 pathogenic Autosomal recessive nonsyndromic hearing loss 4 2023-04-19 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001574741 SCV004295491 pathogenic not provided 2024-01-17 criteria provided, single submitter clinical testing This sequence change falls in intron 9 of the SLC26A4 gene. It does not directly change the encoded amino acid sequence of the SLC26A4 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs111033314, gnomAD 0.01%). This variant has been observed in individual(s) with SLC26A4-related conditions (PMID: 15679828, 28964290, 31387071, 34680964). ClinVar contains an entry for this variant (Variation ID: 43493). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000036424 SCV000060079 pathogenic Rare genetic deafness 2008-11-11 no assertion criteria provided clinical testing
Natera, Inc. RCV001831648 SCV002079989 pathogenic Pendred syndrome 2020-10-14 no assertion criteria provided clinical testing

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