rs5447
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002103.5(GYS1):āc.1246A>Gā(p.Met416Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00969 in 1,613,926 control chromosomes in the GnomAD database, including 426 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_002103.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GYS1 | NM_002103.5 | c.1246A>G | p.Met416Val | missense_variant | 10/16 | ENST00000323798.8 | |
GYS1 | NM_001161587.2 | c.1054A>G | p.Met352Val | missense_variant | 9/15 | ||
GYS1 | NR_027763.2 | n.1261A>G | non_coding_transcript_exon_variant | 9/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GYS1 | ENST00000323798.8 | c.1246A>G | p.Met416Val | missense_variant | 10/16 | 1 | NM_002103.5 | P1 | |
GYS1 | ENST00000263276.6 | c.1054A>G | p.Met352Val | missense_variant | 9/15 | 1 | |||
GYS1 | ENST00000472004.5 | n.1A>G | non_coding_transcript_exon_variant | 1/4 | 3 | ||||
GYS1 | ENST00000496048.1 | n.153A>G | non_coding_transcript_exon_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0148 AC: 2253AN: 152040Hom.: 66 Cov.: 31
GnomAD3 exomes AF: 0.0190 AC: 4768AN: 251470Hom.: 167 AF XY: 0.0185 AC XY: 2511AN XY: 135906
GnomAD4 exome AF: 0.00915 AC: 13378AN: 1461768Hom.: 359 Cov.: 31 AF XY: 0.00948 AC XY: 6891AN XY: 727190
GnomAD4 genome ? AF: 0.0149 AC: 2265AN: 152158Hom.: 67 Cov.: 31 AF XY: 0.0180 AC XY: 1339AN XY: 74376
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 06, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 17, 2017 | - - |
Glycogen storage disease due to muscle and heart glycogen synthase deficiency Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at