rs77938727
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP3BP4_StrongBP6BS1BS2
The NM_000290.4(PGAM2):c.290G>A(p.Gly97Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00052 in 1,613,944 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000290.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGAM2 | ENST00000297283.4 | c.290G>A | p.Gly97Asp | missense_variant | Exon 1 of 3 | 1 | NM_000290.4 | ENSP00000297283.3 | ||
DBNL | ENST00000448521.6 | c.*4324C>T | 3_prime_UTR_variant | Exon 13 of 13 | 1 | NM_001014436.3 | ENSP00000411701.1 |
Frequencies
GnomAD3 genomes AF: 0.000466 AC: 71AN: 152230Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00125 AC: 314AN: 251144Hom.: 5 AF XY: 0.00114 AC XY: 155AN XY: 135818
GnomAD4 exome AF: 0.000525 AC: 768AN: 1461596Hom.: 10 Cov.: 34 AF XY: 0.000525 AC XY: 382AN XY: 727132
GnomAD4 genome AF: 0.000466 AC: 71AN: 152348Hom.: 1 Cov.: 33 AF XY: 0.000510 AC XY: 38AN XY: 74494
ClinVar
Submissions by phenotype
Glycogen storage disease type X Pathogenic:1Uncertain:1Benign:2
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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). 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 rule this variant out of causing disease. Therefore, this variant is classified as benign. -
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not provided Benign:1
This variant is associated with the following publications: (PMID: 6308514, 30445427, 10545043, 22995991, 8447317) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at