chr2-106830191-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001142351.2(ST6GAL2):c.1193G>A(p.Arg398His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,464 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001142351.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ST6GAL2 | ENST00000409382.8 | c.1193G>A | p.Arg398His | missense_variant | Exon 5 of 6 | 1 | NM_001142351.2 | ENSP00000386942.3 | ||
ST6GAL2 | ENST00000361686.8 | c.1193G>A | p.Arg398His | missense_variant | Exon 5 of 6 | 1 | ENSP00000355273.4 | |||
ST6GAL2 | ENST00000409087.3 | c.1193G>A | p.Arg398His | missense_variant | Exon 5 of 6 | 1 | ENSP00000387332.3 | |||
ST6GAL2 | ENST00000361803.3 | c.-113G>A | upstream_gene_variant | 5 | ENSP00000355386.3 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151934Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251172Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135780
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461530Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727090
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151934Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74182
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1193G>A (p.R398H) alteration is located in exon 5 (coding exon 4) of the ST6GAL2 gene. This alteration results from a G to A substitution at nucleotide position 1193, causing the arginine (R) at amino acid position 398 to be replaced by a histidine (H). 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