rs201556175
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_006446.5(SLCO1B1):c.1794G>A(p.Thr598=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00196 in 1,612,092 control chromosomes in the GnomAD database, including 89 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0013 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 86 hom. )
Consequence
SLCO1B1
NM_006446.5 synonymous
NM_006446.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.78
Genes affected
SLCO1B1 (HGNC:10959): (solute carrier organic anion transporter family member 1B1) 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 numerous endogenous compounds including bilirubin, 17-beta-glucuronosyl estradiol and leukotriene C4. This protein is also involved in the removal of drug compounds such as statins, bromosulfophthalein and rifampin from the blood into the hepatocytes. Polymorphisms in the gene encoding this protein are associated with impaired transporter function. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 12-21224768-G-A is Benign according to our data. Variant chr12-21224768-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 307958.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-21224768-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-1.78 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00127 (194/152168) while in subpopulation SAS AF= 0.0394 (190/4824). AF 95% confidence interval is 0.0348. There are 3 homozygotes in gnomad4. There are 145 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 194 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1B1 | NM_006446.5 | c.1794G>A | p.Thr598= | synonymous_variant | 14/15 | ENST00000256958.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1B1 | ENST00000256958.3 | c.1794G>A | p.Thr598= | synonymous_variant | 14/15 | 1 | NM_006446.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00128 AC: 194AN: 152052Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00410 AC: 1029AN: 251148Hom.: 28 AF XY: 0.00554 AC XY: 752AN XY: 135754
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GnomAD4 exome AF: 0.00203 AC: 2959AN: 1459924Hom.: 86 Cov.: 29 AF XY: 0.00290 AC XY: 2107AN XY: 726356
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Rotor syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational 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