chr12-20875266-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_019844.4(SLCO1B3):c.759T>C(p.Arg253=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R253R) has been classified as Benign.
Frequency
Consequence
NM_019844.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1B3 | NM_019844.4 | c.759T>C | p.Arg253= | synonymous_variant | 9/16 | ENST00000381545.8 | |
SLCO1B3-SLCO1B7 | NM_001371097.1 | c.759T>C | p.Arg253= | synonymous_variant | 7/16 | ||
SLCO1B3 | NM_001349920.2 | c.675T>C | p.Arg225= | synonymous_variant | 7/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1B3 | ENST00000381545.8 | c.759T>C | p.Arg253= | synonymous_variant | 9/16 | 2 | NM_019844.4 | P1 | |
SLCO1B3 | ENST00000261196.6 | c.759T>C | p.Arg253= | synonymous_variant | 7/14 | 1 | P1 | ||
SLCO1B3 | ENST00000540853.5 | c.759T>C | p.Arg253= | synonymous_variant | 8/8 | 1 | |||
SLCO1B3 | ENST00000544370.1 | c.231T>C | p.Arg77= | synonymous_variant | 3/10 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 249860Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135132
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460084Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726402
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at