11-66042593-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033036.3(GAL3ST3):c.1210G>A(p.Gly404Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000221 in 1,535,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033036.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GAL3ST3 | ENST00000312006.5 | c.1210G>A | p.Gly404Ser | missense_variant | Exon 3 of 3 | 1 | NM_033036.3 | ENSP00000308591.3 | ||
GAL3ST3 | ENST00000527878.1 | c.1210G>A | p.Gly404Ser | missense_variant | Exon 2 of 2 | 1 | ENSP00000434829.1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 151914Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000150 AC: 20AN: 133100Hom.: 0 AF XY: 0.000137 AC XY: 10AN XY: 72962
GnomAD4 exome AF: 0.000231 AC: 320AN: 1383920Hom.: 0 Cov.: 33 AF XY: 0.000231 AC XY: 158AN XY: 683064
GnomAD4 genome AF: 0.000125 AC: 19AN: 151914Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74184
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1210G>A (p.G404S) alteration is located in exon 3 (coding exon 2) of the GAL3ST3 gene. This alteration results from a G to A substitution at nucleotide position 1210, causing the glycine (G) at amino acid position 404 to be replaced by a serine (S). 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