17-76574442-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006456.3(ST6GALNAC2):c.284A>T(p.Asp95Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,612,806 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_006456.3 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 |
---|---|---|---|---|---|---|---|
ST6GALNAC2 | NM_006456.3 | c.284A>T | p.Asp95Val | missense_variant | 3/9 | ENST00000225276.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST6GALNAC2 | ENST00000225276.10 | c.284A>T | p.Asp95Val | missense_variant | 3/9 | 1 | NM_006456.3 | P1 | |
SNHG16 | ENST00000701062.1 | n.194+13044T>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000661 AC: 1AN: 151264Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249946Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135470
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461542Hom.: 0 Cov.: 42 AF XY: 0.0000138 AC XY: 10AN XY: 727060
GnomAD4 genome ? AF: 0.00000661 AC: 1AN: 151264Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73838
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.284A>T (p.D95V) alteration is located in exon 3 (coding exon 3) of the ST6GALNAC2 gene. This alteration results from a A to T substitution at nucleotide position 284, causing the aspartic acid (D) at amino acid position 95 to be replaced by a valine (V). 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