rs2084543
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_001178015.2(SLC4A10):c.393C>T(p.Asp131=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0713 in 1,613,532 control chromosomes in the GnomAD database, including 4,603 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.061 ( 368 hom., cov: 32)
Exomes 𝑓: 0.072 ( 4235 hom. )
Consequence
SLC4A10
NM_001178015.2 synonymous
NM_001178015.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.322
Genes affected
SLC4A10 (HGNC:13811): (solute carrier family 4 member 10) This gene belongs to a small family of sodium-coupled bicarbonate transporters (NCBTs) that regulate the intracellular pH of neurons, the secretion of bicarbonate ions across the choroid plexus, and the pH of the brain extracellular fluid. The protein encoded by this gene was initially identified as a sodium-driven chloride bicarbonate exchanger (NCBE) though there is now evidence that its sodium/bicarbonate cotransport activity is independent of any chloride ion countertransport under physiological conditions. This gene is now classified as a member A10 of the SLC4 family of transmembrane solute carriers. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.27).
BP6
?
Variant 2-161839904-C-T is Benign according to our data. Variant chr2-161839904-C-T is described in ClinVar as [Benign]. Clinvar id is 586611.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.322 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A10 | NM_001178015.2 | c.393C>T | p.Asp131= | synonymous_variant | 4/27 | ENST00000446997.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A10 | ENST00000446997.6 | c.393C>T | p.Asp131= | synonymous_variant | 4/27 | 1 | NM_001178015.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0607 AC: 9230AN: 151984Hom.: 367 Cov.: 32
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GnomAD3 exomes AF: 0.0736 AC: 18345AN: 249270Hom.: 831 AF XY: 0.0758 AC XY: 10252AN XY: 135228
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GnomAD4 exome AF: 0.0724 AC: 105851AN: 1461430Hom.: 4235 Cov.: 31 AF XY: 0.0735 AC XY: 53468AN XY: 727010
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GnomAD4 genome ? AF: 0.0607 AC: 9234AN: 152102Hom.: 368 Cov.: 32 AF XY: 0.0637 AC XY: 4735AN XY: 74344
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 07, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -8
Find out detailed SpliceAI scores and Pangolin per-transcript scores at