rs11045585
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_019844.4(SLCO1B3):c.1683-5676A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,162 control chromosomes in the GnomAD database, including 2,283 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 0.17 ( 2283 hom., cov: 32)
Consequence
SLCO1B3
NM_019844.4 intron
NM_019844.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.744
Genes affected
SLCO1B3 (HGNC:10961): (solute carrier organic anion transporter family member 1B3) This gene encodes a liver-specific member of the organic anion transporter family. The encoded protein is a transmembrane receptor that mediates the sodium-independent uptake of endogenous and xenobiotic compounds and plays a critical role in bile acid and bilirubin transport. Mutations in this gene are a cause of Rotor type hyperbilirubinemia. Alternative splicing of this gene and the use of alternative promoters results in transcript variants encoding different isoforms that differ in their tissue specificity. [provided by RefSeq, Mar 2017]
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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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLCO1B3 | NM_019844.4 | c.1683-5676A>G | intron_variant | ENST00000381545.8 | NP_062818.1 | |||
SLCO1B3-SLCO1B7 | NM_001371097.1 | c.1683-5676A>G | intron_variant | NP_001358026.1 | ||||
SLCO1B3 | NM_001349920.2 | c.1599-5676A>G | intron_variant | NP_001336849.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO1B3 | ENST00000381545.8 | c.1683-5676A>G | intron_variant | 2 | NM_019844.4 | ENSP00000370956 | P1 | |||
SLCO1B3 | ENST00000261196.6 | c.1683-5676A>G | intron_variant | 1 | ENSP00000261196 | P1 | ||||
SLCO1B3 | ENST00000544370.1 | c.1155-5676A>G | intron_variant | 5 | ENSP00000443225 |
Frequencies
GnomAD3 genomes AF: 0.167 AC: 25366AN: 152044Hom.: 2280 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.167 AC: 25379AN: 152162Hom.: 2283 Cov.: 32 AF XY: 0.171 AC XY: 12703AN XY: 74384
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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