rs3793336
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003040.4(SLC4A2):c.579-733G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,044 control chromosomes in the GnomAD database, including 57,227 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 0.87 ( 57227 hom., cov: 31)
Consequence
SLC4A2
NM_003040.4 intron
NM_003040.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.786
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=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A2 | NM_003040.4 | c.579-733G>A | intron_variant | ENST00000413384.7 | |||
SLC4A2 | NM_001199692.3 | c.579-733G>A | intron_variant | ||||
SLC4A2 | NM_001199693.1 | c.552-733G>A | intron_variant | ||||
SLC4A2 | NM_001199694.2 | c.537-733G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A2 | ENST00000413384.7 | c.579-733G>A | intron_variant | 1 | NM_003040.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.867 AC: 131729AN: 151926Hom.: 57176 Cov.: 31
GnomAD3 genomes
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131729
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151926
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.867 AC: 131837AN: 152044Hom.: 57227 Cov.: 31 AF XY: 0.867 AC XY: 64434AN XY: 74312
GnomAD4 genome
?
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131837
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152044
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31
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64434
AN XY:
74312
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3069
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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