chr12-21536998-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021957.4(GYS2):c.2068G>T(p.Val690Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,613,876 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V690I) has been classified as Uncertain significance.
Frequency
Consequence
NM_021957.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GYS2 | NM_021957.4 | c.2068G>T | p.Val690Phe | missense_variant | 16/16 | ENST00000261195.3 | |
LOC124902896 | XR_007063240.1 | n.519-48C>A | intron_variant, non_coding_transcript_variant | ||||
GYS2 | XM_024448960.2 | c.2068G>T | p.Val690Phe | missense_variant | 16/17 | ||
GYS2 | XM_006719063.4 | c.1837G>T | p.Val613Phe | missense_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GYS2 | ENST00000261195.3 | c.2068G>T | p.Val690Phe | missense_variant | 16/16 | 1 | NM_021957.4 | P1 | |
SPX | ENST00000537527.1 | n.472-48C>A | intron_variant, non_coding_transcript_variant | 3 | |||||
SPX | ENST00000649016.1 | n.529-48C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000710 AC: 108AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251154Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135738
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461674Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727162
GnomAD4 genome ? AF: 0.000769 AC: 117AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.000699 AC XY: 52AN XY: 74426
ClinVar
Submissions by phenotype
Glycogen storage disorder due to hepatic glycogen synthase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at