rs754862840
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PM4_SupportingBP6
The NM_019844.4(SLCO1B3):c.141_143delTAT(p.Ile47del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000819 in 1,611,546 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_019844.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLCO1B3 | NM_019844.4 | c.141_143delTAT | p.Ile47del | disruptive_inframe_deletion | Exon 4 of 16 | ENST00000381545.8 | NP_062818.1 | |
SLCO1B3-SLCO1B7 | NM_001371097.1 | c.141_143delTAT | p.Ile47del | disruptive_inframe_deletion | Exon 2 of 16 | NP_001358026.1 | ||
SLCO1B3 | NM_001349920.2 | c.57_59delTAT | p.Ile19del | disruptive_inframe_deletion | Exon 2 of 14 | NP_001336849.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO1B3 | ENST00000381545.8 | c.141_143delTAT | p.Ile47del | disruptive_inframe_deletion | Exon 4 of 16 | 2 | NM_019844.4 | ENSP00000370956.4 | ||
SLCO1B3-SLCO1B7 | ENST00000540229.1 | c.141_143delTAT | p.Ile47del | disruptive_inframe_deletion | Exon 2 of 16 | 2 | ENSP00000441269.1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251004Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135684
GnomAD4 exome AF: 0.0000802 AC: 117AN: 1459372Hom.: 0 AF XY: 0.0000813 AC XY: 59AN XY: 726074
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74336
ClinVar
Submissions by phenotype
SLCO1B3-related disorder Benign:1
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