2-106843583-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142351.2(ST6GAL2):c.395T>C(p.Phe132Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,613,840 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 Uncertain significance (★).
Frequency
Consequence
NM_001142351.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST6GAL2 | NM_001142351.2 | c.395T>C | p.Phe132Ser | missense_variant | 2/6 | ENST00000409382.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST6GAL2 | ENST00000409382.8 | c.395T>C | p.Phe132Ser | missense_variant | 2/6 | 1 | NM_001142351.2 | P1 | |
ST6GAL2 | ENST00000361686.8 | c.395T>C | p.Phe132Ser | missense_variant | 2/6 | 1 | P1 | ||
ST6GAL2 | ENST00000409087.3 | c.395T>C | p.Phe132Ser | missense_variant | 2/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250314Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135762
GnomAD4 exome AF: 0.0000472 AC: 69AN: 1461742Hom.: 0 Cov.: 32 AF XY: 0.0000385 AC XY: 28AN XY: 727178
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.395T>C (p.F132S) alteration is located in exon 2 (coding exon 1) of the ST6GAL2 gene. This alteration results from a T to C substitution at nucleotide position 395, causing the phenylalanine (F) at amino acid position 132 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