17-76574409-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006456.3(ST6GALNAC2):c.317G>A(p.Ser106Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000899 in 1,613,714 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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
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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.317G>A | p.Ser106Asn | missense_variant | 3/9 | ENST00000225276.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST6GALNAC2 | ENST00000225276.10 | c.317G>A | p.Ser106Asn | missense_variant | 3/9 | 1 | NM_006456.3 | P1 | |
SNHG16 | ENST00000701062.1 | n.194+13011C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249844Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135414
GnomAD4 exome AF: 0.0000958 AC: 140AN: 1461528Hom.: 0 Cov.: 41 AF XY: 0.0000894 AC XY: 65AN XY: 727058
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 30 AF XY: 0.0000404 AC XY: 3AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.317G>A (p.S106N) alteration is located in exon 3 (coding exon 3) of the ST6GALNAC2 gene. This alteration results from a G to A substitution at nucleotide position 317, causing the serine (S) at amino acid position 106 to be replaced by an asparagine (N). 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