rs2303930
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003040.4(SLC4A2):c.218-65A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 1,563,010 control chromosomes in the GnomAD database, including 98,054 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 0.34 ( 8459 hom., cov: 25)
Exomes 𝑓: 0.35 ( 89595 hom. )
Consequence
SLC4A2
NM_003040.4 intron
NM_003040.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.47
Genes affected
SLC4A2 (HGNC:11028): (solute carrier family 4 member 2) This gene encodes a member of the anion exchanger family of membrane transport proteins. The encoded protein regulates intracellular pH, biliary bicarbonate secretion, and chloride uptake. Reduced expression of this gene may be associated with primary biliary cirrhosis (PBC) in human patients, while differential expression of this gene may be associated with malignant hepatocellular carcinoma, colon and gastric cancers. [provided by RefSeq, Nov 2016]
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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 (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A2 | NM_003040.4 | c.218-65A>G | intron_variant | ENST00000413384.7 | |||
SLC4A2 | NM_001199692.3 | c.218-65A>G | intron_variant | ||||
SLC4A2 | NM_001199693.1 | c.191-65A>G | intron_variant | ||||
SLC4A2 | NM_001199694.2 | c.176-65A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A2 | ENST00000413384.7 | c.218-65A>G | intron_variant | 1 | NM_003040.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.338 AC: 49076AN: 145220Hom.: 8454 Cov.: 25
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GnomAD4 exome AF: 0.353 AC: 500682AN: 1417694Hom.: 89595 Cov.: 34 AF XY: 0.352 AC XY: 246462AN XY: 699732
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GnomAD4 genome ? AF: 0.338 AC: 49111AN: 145316Hom.: 8459 Cov.: 25 AF XY: 0.339 AC XY: 23954AN XY: 70716
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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