NM_198999.3:c.1311+241G>A
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_StrongBS1
The NM_198999.3(SLC26A5):c.1311+241G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 152,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0011 ( 0 hom., cov: 31)
Consequence
SLC26A5
NM_198999.3 intron
NM_198999.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.07
Genes affected
SLC26A5 (HGNC:9359): (solute carrier family 26 member 5) This gene encodes a member of the SLC26A/SulP transporter family. The protein functions as a molecular motor in motile outer hair cells (OHCs) of the cochlea, inducing changes in cell length that act to amplify sound levels. The transmembrane protein is an incomplete anion transporter, and does not allow anions to cross the cell membrane but instead undergoes a conformational change in response to changes in intracellular Cl- levels that results in a change in cell length. The protein functions at microsecond rates, which is several orders of magnitude faster than conventional molecular motor proteins. Mutations in this gene are potential candidates for causing neurosensory deafness. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00109 (166/152124) while in subpopulation NFE AF= 0.00196 (133/68010). AF 95% confidence interval is 0.00168. There are 0 homozygotes in gnomad4. There are 68 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SLC26A5 | ENST00000306312.8 | c.1311+241G>A | intron_variant | Intron 12 of 19 | 1 | NM_198999.3 | ENSP00000304783.3 | |||
| SLC26A5 | ENST00000393727.5 | c.1311+241G>A | intron_variant | Intron 10 of 17 | 1 | ENSP00000377328.1 | ||||
| SLC26A5 | ENST00000393723.2 | c.1311+241G>A | intron_variant | Intron 10 of 16 | 1 | ENSP00000377324.1 |
Frequencies
GnomAD3 genomes 0.00109 AC: 166AN: 152006Hom.: 0 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00109 AC: 166AN: 152124Hom.: 0 Cov.: 31 AF XY: 0.000914 AC XY: 68AN XY: 74390
GnomAD4 genome
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31
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at