2-108252371-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001320878.2(SULT1C3):c.179C>A(p.Thr60Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000373 in 1,608,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001320878.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SULT1C3 | ENST00000681802.2 | c.179C>A | p.Thr60Lys | missense_variant | Exon 3 of 8 | NM_001320878.2 | ENSP00000505748.1 | |||
SULT1C3 | ENST00000329106.3 | c.179C>A | p.Thr60Lys | missense_variant | Exon 3 of 8 | 2 | ENSP00000333310.2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152002Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248908Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134614
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1456264Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 2AN XY: 724448
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74232
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.179C>A (p.T60K) alteration is located in exon 2 (coding exon 2) of the SULT1C3 gene. This alteration results from a C to A substitution at nucleotide position 179, causing the threonine (T) at amino acid position 60 to be replaced by a lysine (K). 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