NM_006927.4:c.271G>A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006927.4(ST3GAL2):c.271G>A(p.Gly91Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,322 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 Likely benign (★).
Frequency
Consequence
NM_006927.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ST3GAL2 | NM_006927.4 | c.271G>A | p.Gly91Ser | missense_variant | Exon 2 of 7 | ENST00000342907.3 | NP_008858.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ST3GAL2 | ENST00000342907.3 | c.271G>A | p.Gly91Ser | missense_variant | Exon 2 of 7 | 5 | NM_006927.4 | ENSP00000345477.2 | ||
ST3GAL2 | ENST00000393640.8 | c.271G>A | p.Gly91Ser | missense_variant | Exon 1 of 6 | 1 | ENSP00000377257.4 | |||
ENSG00000260111 | ENST00000566960.1 | n.211-863C>T | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249486Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135230
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461080Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726828
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74378
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at