chr17-76574472-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_006456.3(ST6GALNAC2):c.254A>G(p.Asn85Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,496 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
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST6GALNAC2 | NM_006456.3 | c.254A>G | p.Asn85Ser | missense_variant | 3/9 | ENST00000225276.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST6GALNAC2 | ENST00000225276.10 | c.254A>G | p.Asn85Ser | missense_variant | 3/9 | 1 | NM_006456.3 | P1 | |
SNHG16 | ENST00000701062.1 | n.194+13074T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151790Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250386Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135660
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461706Hom.: 0 Cov.: 41 AF XY: 0.0000303 AC XY: 22AN XY: 727154
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151790Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74116
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2023 | The c.254A>G (p.N85S) alteration is located in exon 3 (coding exon 3) of the ST6GALNAC2 gene. This alteration results from a A to G substitution at nucleotide position 254, causing the asparagine (N) at amino acid position 85 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