chr15-92444668-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006011.4(ST8SIA2):c.581G>A(p.Arg194Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,614,216 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_006011.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ST8SIA2 | NM_006011.4 | c.581G>A | p.Arg194Gln | missense_variant | 5/6 | ENST00000268164.8 | NP_006002.1 | |
ST8SIA2 | NM_001330416.2 | c.518G>A | p.Arg173Gln | missense_variant | 4/5 | NP_001317345.1 | ||
ST8SIA2 | XM_017022642.2 | c.644G>A | p.Arg215Gln | missense_variant | 5/6 | XP_016878131.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ST8SIA2 | ENST00000268164.8 | c.581G>A | p.Arg194Gln | missense_variant | 5/6 | 1 | NM_006011.4 | ENSP00000268164 | P1 | |
ST8SIA2 | ENST00000539113.5 | c.518G>A | p.Arg173Gln | missense_variant | 4/5 | 1 | ENSP00000437382 | |||
ST8SIA2 | ENST00000555434.1 | c.452G>A | p.Arg151Gln | missense_variant | 4/5 | 5 | ENSP00000450851 | |||
ST8SIA2 | ENST00000556382.1 | n.351G>A | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000680 AC: 17AN: 250164Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135344
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727244
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2022 | The c.581G>A (p.R194Q) alteration is located in exon 5 (coding exon 5) of the ST8SIA2 gene. This alteration results from a G to A substitution at nucleotide position 581, causing the arginine (R) at amino acid position 194 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at