rs3764006
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_019844.4(SLCO1B3):c.1833G>A(p.Gly611=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 1,561,636 control chromosomes in the GnomAD database, including 582,197 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.71 ( 42957 hom., cov: 32)
Exomes 𝑓: 0.87 ( 539240 hom. )
Consequence
SLCO1B3
NM_019844.4 synonymous
NM_019844.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.38
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 12-20901435-G-A is Benign according to our data. Variant chr12-20901435-G-A is described in ClinVar as [Benign]. Clinvar id is 440286.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-20901435-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-1.38 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1B3 | NM_019844.4 | c.1833G>A | p.Gly611= | synonymous_variant | 15/16 | ENST00000381545.8 | |
SLCO1B3-SLCO1B7 | NM_001371097.1 | c.1833G>A | p.Gly611= | synonymous_variant | 13/16 | ||
LOC124902894 | XM_047429949.1 | c.-90G>A | 5_prime_UTR_variant | 1/10 | |||
SLCO1B3 | NM_001349920.2 | c.1749G>A | p.Gly583= | synonymous_variant | 13/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1B3 | ENST00000381545.8 | c.1833G>A | p.Gly611= | synonymous_variant | 15/16 | 2 | NM_019844.4 | P1 | |
SLCO1B3 | ENST00000261196.6 | c.1833G>A | p.Gly611= | synonymous_variant | 13/14 | 1 | P1 | ||
SLCO1B3 | ENST00000544370.1 | c.1305G>A | p.Gly435= | synonymous_variant | 9/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.714 AC: 108446AN: 151900Hom.: 42953 Cov.: 32
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GnomAD3 exomes AF: 0.817 AC: 171302AN: 209728Hom.: 72283 AF XY: 0.836 AC XY: 95699AN XY: 114476
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GnomAD4 exome AF: 0.870 AC: 1225839AN: 1409618Hom.: 539240 Cov.: 28 AF XY: 0.873 AC XY: 611656AN XY: 700460
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GnomAD4 genome ? AF: 0.714 AC: 108481AN: 152018Hom.: 42957 Cov.: 32 AF XY: 0.712 AC XY: 52881AN XY: 74322
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Rotor syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 30, 2023 | - - |
Computational scores
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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