rs3796109
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_133478.3(SLC4A5):c.2439G>A(p.Thr813=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0445 in 1,611,466 control chromosomes in the GnomAD database, including 3,247 homozygotes. 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 0.074 ( 726 hom., cov: 32)
Exomes 𝑓: 0.041 ( 2521 hom. )
Consequence
SLC4A5
NM_133478.3 synonymous
NM_133478.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -8.92
Genes affected
SLC4A5 (HGNC:18168): (solute carrier family 4 member 5) This gene encodes a member of the sodium bicarbonate cotransporter (NBC) family, part of the bicarbonate transporter superfamily. Sodium bicarbonate cotransporters are involved in intracellular pH regulation and electroneural or electrogenic sodium bicarbonate transport. This protein is thought to be an integral membrane protein. Multiple transcript variants encoding different isoforms have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]
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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=-0.56).
BP7
?
Synonymous conserved (PhyloP=-8.92 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A5 | NM_133478.3 | c.2439G>A | p.Thr813= | synonymous_variant | 23/31 | ENST00000394019.7 | |
SLC4A5 | NM_021196.3 | c.2439G>A | p.Thr813= | synonymous_variant | 18/26 | ||
SLC4A5 | NM_001386136.1 | c.2091G>A | p.Thr697= | synonymous_variant | 17/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A5 | ENST00000394019.7 | c.2439G>A | p.Thr813= | synonymous_variant | 23/31 | 5 | NM_133478.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0740 AC: 11259AN: 152144Hom.: 719 Cov.: 32
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GnomAD3 exomes AF: 0.0696 AC: 17309AN: 248534Hom.: 1368 AF XY: 0.0602 AC XY: 8095AN XY: 134454
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GnomAD4 exome AF: 0.0414 AC: 60464AN: 1459204Hom.: 2521 Cov.: 31 AF XY: 0.0395 AC XY: 28685AN XY: 725604
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GnomAD4 genome ? AF: 0.0741 AC: 11288AN: 152262Hom.: 726 Cov.: 32 AF XY: 0.0741 AC XY: 5519AN XY: 74450
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at