rs61612406
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_019844.4(SLCO1B3):āc.11A>Gā(p.His4Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,590,812 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_019844.4 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 | UniProt |
---|---|---|---|---|---|---|---|
SLCO1B3 | NM_019844.4 | c.11A>G | p.His4Arg | missense_variant | 3/16 | ENST00000381545.8 | |
SLCO1B3-SLCO1B7 | NM_001371097.1 | c.11A>G | p.His4Arg | missense_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1B3 | ENST00000381545.8 | c.11A>G | p.His4Arg | missense_variant | 3/16 | 2 | NM_019844.4 | P1 | |
SLCO1B3 | ENST00000261196.6 | c.11A>G | p.His4Arg | missense_variant | 1/14 | 1 | P1 | ||
SLCO1B3 | ENST00000540853.5 | c.11A>G | p.His4Arg | missense_variant | 2/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00658 AC: 1001AN: 152216Hom.: 10 Cov.: 33
GnomAD3 exomes AF: 0.00166 AC: 393AN: 237418Hom.: 6 AF XY: 0.00118 AC XY: 152AN XY: 128914
GnomAD4 exome AF: 0.000636 AC: 915AN: 1438478Hom.: 12 Cov.: 28 AF XY: 0.000534 AC XY: 382AN XY: 715812
GnomAD4 genome ? AF: 0.00670 AC: 1021AN: 152334Hom.: 13 Cov.: 33 AF XY: 0.00664 AC XY: 495AN XY: 74506
ClinVar
Submissions by phenotype
Rotor syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 14, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Oct 11, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at