12-20815826-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019844.4(SLCO1B3):c.84+4G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000128 in 1,558,364 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019844.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLCO1B3 | NM_019844.4 | c.84+4G>T | splice_region_variant, intron_variant | Intron 3 of 15 | ENST00000381545.8 | NP_062818.1 | ||
SLCO1B3-SLCO1B7 | NM_001371097.1 | c.84+4G>T | splice_region_variant, intron_variant | Intron 1 of 15 | NP_001358026.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO1B3 | ENST00000381545.8 | c.84+4G>T | splice_region_variant, intron_variant | Intron 3 of 15 | 2 | NM_019844.4 | ENSP00000370956.4 | |||
SLCO1B3-SLCO1B7 | ENST00000540229.1 | c.84+4G>T | splice_region_variant, intron_variant | Intron 1 of 15 | 2 | ENSP00000441269.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152120Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000446 AC: 1AN: 224232Hom.: 0 AF XY: 0.00000821 AC XY: 1AN XY: 121774
GnomAD4 exome AF: 7.11e-7 AC: 1AN: 1406244Hom.: 0 Cov.: 24 AF XY: 0.00000143 AC XY: 1AN XY: 699702
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152120Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74302
ClinVar
Submissions by phenotype
Rotor syndrome Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at