rs369069984
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_021957.4(GYS2):c.1745G>A(p.Arg582Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,613,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R582R) has been classified as Likely benign.
Frequency
Consequence
NM_021957.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GYS2 | NM_021957.4 | c.1745G>A | p.Arg582Lys | missense_variant | 14/16 | ENST00000261195.3 | |
GYS2 | XM_024448960.2 | c.1745G>A | p.Arg582Lys | missense_variant | 14/17 | ||
GYS2 | XM_006719063.4 | c.1514G>A | p.Arg505Lys | missense_variant | 13/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GYS2 | ENST00000261195.3 | c.1745G>A | p.Arg582Lys | missense_variant | 14/16 | 1 | NM_021957.4 | P1 | |
SPX | ENST00000649016.1 | n.3957C>T | non_coding_transcript_exon_variant | 5/5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152116Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251354Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135838
GnomAD4 exome AF: 0.000114 AC: 166AN: 1461792Hom.: 0 Cov.: 31 AF XY: 0.000102 AC XY: 74AN XY: 727214
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152116Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74296
ClinVar
Submissions by phenotype
Glycogen storage disorder due to hepatic glycogen synthase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at