2-74222998-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_133478.3(SLC4A5):c.3247-46A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,356,192 control chromosomes in the GnomAD database, including 30,310 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 0.29 ( 9780 hom., cov: 31)
Exomes 𝑓: 0.14 ( 20530 hom. )
Consequence
SLC4A5
NM_133478.3 intron
NM_133478.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.145
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A5 | NM_133478.3 | c.3247-46A>G | intron_variant | ENST00000394019.7 | |||
SLC4A5 | NM_001386136.1 | c.2899-46A>G | intron_variant | ||||
SLC4A5 | NM_021196.3 | c.3295-46A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A5 | ENST00000394019.7 | c.3247-46A>G | intron_variant | 5 | NM_133478.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.286 AC: 43238AN: 151446Hom.: 9744 Cov.: 31
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GnomAD3 exomes AF: 0.261 AC: 42006AN: 160688Hom.: 8215 AF XY: 0.240 AC XY: 20513AN XY: 85414
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GnomAD4 exome AF: 0.142 AC: 171490AN: 1204636Hom.: 20530 Cov.: 16 AF XY: 0.140 AC XY: 84783AN XY: 604310
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GnomAD4 genome AF: 0.286 AC: 43323AN: 151556Hom.: 9780 Cov.: 31 AF XY: 0.284 AC XY: 21046AN XY: 74102
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ClinVar
Not reported inComputational scores
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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