2-108247199-C-A
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001320878.2(SULT1C3):c.5C>A(p.Ala2Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000735 in 1,361,314 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A2V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001320878.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SULT1C3 | ENST00000681802.2 | c.5C>A | p.Ala2Glu | missense_variant | Exon 2 of 8 | NM_001320878.2 | ENSP00000505748.1 | |||
SULT1C3 | ENST00000329106.3 | c.5C>A | p.Ala2Glu | missense_variant | Exon 2 of 8 | 2 | ENSP00000333310.2 | |||
ENSG00000294676 | ENST00000725207.1 | n.168-11336G>T | intron_variant | Intron 1 of 1 | ||||||
ENSG00000294676 | ENST00000725208.1 | n.43-11336G>T | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 7.35e-7 AC: 1AN: 1361314Hom.: 0 Cov.: 32 AF XY: 0.00000149 AC XY: 1AN XY: 670526 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at