chr11-66042689-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.1114G>A(p.Gly372Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000456 in 1,533,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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.1114G>A | p.Gly372Ser | missense_variant | Exon 3 of 3 | 1 | NM_033036.3 | ENSP00000308591.3 | ||
GAL3ST3 | ENST00000527878.1 | c.1114G>A | p.Gly372Ser | missense_variant | Exon 2 of 2 | 1 | ENSP00000434829.1 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151822Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000434 AC: 6AN: 1382094Hom.: 0 Cov.: 33 AF XY: 0.00000440 AC XY: 3AN XY: 681966
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151822Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74152
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1114G>A (p.G372S) 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 1114, causing the glycine (G) at amino acid position 372 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