chr12-20732995-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017435.5(SLCO1C1):c.1273G>A(p.Ala425Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000626 in 1,613,794 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A425A) has been classified as Benign.
Frequency
Consequence
NM_017435.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1C1 | NM_017435.5 | c.1273G>A | p.Ala425Thr | missense_variant | 10/15 | ENST00000266509.7 | |
SLCO1C1 | NM_001145946.2 | c.1273G>A | p.Ala425Thr | missense_variant | 11/16 | ||
SLCO1C1 | NM_001145945.2 | c.1126G>A | p.Ala376Thr | missense_variant | 10/15 | ||
SLCO1C1 | NM_001145944.2 | c.919G>A | p.Ala307Thr | missense_variant | 8/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1C1 | ENST00000266509.7 | c.1273G>A | p.Ala425Thr | missense_variant | 10/15 | 1 | NM_017435.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000139 AC: 35AN: 251126Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135736
GnomAD4 exome AF: 0.0000671 AC: 98AN: 1461596Hom.: 1 Cov.: 30 AF XY: 0.0000949 AC XY: 69AN XY: 727082
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74404
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2023 | The c.1273G>A (p.A425T) alteration is located in exon 11 (coding exon 9) of the SLCO1C1 gene. This alteration results from a G to A substitution at nucleotide position 1273, causing the alanine (A) at amino acid position 425 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at