rs34671512
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006446.5(SLCO1B1):āc.1929A>Cā(p.Leu643Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0503 in 1,592,164 control chromosomes in the GnomAD database, including 2,239 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_006446.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLCO1B1 | NM_006446.5 | c.1929A>C | p.Leu643Phe | missense_variant | 15/15 | ENST00000256958.3 | NP_006437.3 | |
LOC124902895 | XR_007063239.1 | n.87-4743T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO1B1 | ENST00000256958.3 | c.1929A>C | p.Leu643Phe | missense_variant | 15/15 | 1 | NM_006446.5 | ENSP00000256958.2 |
Frequencies
GnomAD3 genomes AF: 0.0534 AC: 8124AN: 152044Hom.: 238 Cov.: 32
GnomAD3 exomes AF: 0.0453 AC: 11209AN: 247440Hom.: 285 AF XY: 0.0461 AC XY: 6186AN XY: 134330
GnomAD4 exome AF: 0.0500 AC: 72012AN: 1440000Hom.: 1998 Cov.: 27 AF XY: 0.0503 AC XY: 36059AN XY: 717384
GnomAD4 genome AF: 0.0535 AC: 8137AN: 152164Hom.: 241 Cov.: 32 AF XY: 0.0526 AC XY: 3913AN XY: 74412
ClinVar
Submissions by phenotype
Rotor syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 27, 2023 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | This variant is associated with the following publications: (PMID: 22147369) - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
SLCO1B1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 21, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at