chr12-20737156-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017435.5(SLCO1C1):c.1432T>A(p.Ser478Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000449 in 1,559,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S478L) has been classified as Uncertain significance.
Frequency
Consequence
NM_017435.5 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1C1 | NM_017435.5 | c.1432T>A | p.Ser478Thr | missense_variant | 11/15 | ENST00000266509.7 | |
SLCO1C1 | NM_001145946.2 | c.1432T>A | p.Ser478Thr | missense_variant | 12/16 | ||
SLCO1C1 | NM_001145945.2 | c.1285T>A | p.Ser429Thr | missense_variant | 11/15 | ||
SLCO1C1 | NM_001145944.2 | c.1078T>A | p.Ser360Thr | missense_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1C1 | ENST00000266509.7 | c.1432T>A | p.Ser478Thr | missense_variant | 11/15 | 1 | NM_017435.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000984 AC: 2AN: 203150Hom.: 0 AF XY: 0.0000180 AC XY: 2AN XY: 110998
GnomAD4 exome AF: 0.00000426 AC: 6AN: 1407664Hom.: 0 Cov.: 30 AF XY: 0.00000715 AC XY: 5AN XY: 698862
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2022 | The c.1432T>A (p.S478T) alteration is located in exon 12 (coding exon 10) of the SLCO1C1 gene. This alteration results from a T to A substitution at nucleotide position 1432, causing the serine (S) at amino acid position 478 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