rs113806080
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP3BP4_StrongBP6_Very_StrongBS1BS2
The NM_005609.4(PYGM):c.2009C>T(p.Ala670Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00419 in 1,614,162 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005609.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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PYGM | ENST00000164139.4 | c.2009C>T | p.Ala670Val | missense_variant | Exon 17 of 20 | 1 | NM_005609.4 | ENSP00000164139.3 | ||
PYGM | ENST00000377432.7 | c.1745C>T | p.Ala582Val | missense_variant | Exon 15 of 18 | 2 | ENSP00000366650.3 |
Frequencies
GnomAD3 genomes AF: 0.00427 AC: 650AN: 152188Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00490 AC: 1231AN: 251412Hom.: 9 AF XY: 0.00481 AC XY: 654AN XY: 135896
GnomAD4 exome AF: 0.00419 AC: 6119AN: 1461856Hom.: 22 Cov.: 32 AF XY: 0.00413 AC XY: 3003AN XY: 727228
GnomAD4 genome AF: 0.00427 AC: 650AN: 152306Hom.: 3 Cov.: 32 AF XY: 0.00536 AC XY: 399AN XY: 74482
ClinVar
Submissions by phenotype
Glycogen storage disease, type V Benign:6
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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). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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not provided Benign:3
This variant is associated with the following publications: (PMID: 24503134, 20108426, 33111339) -
PYGM: PP3, BS2 -
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not specified Benign:2
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PYGM-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at