chr2-168908036-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_021176.3(G6PC2):c.1025C>G(p.Ser342Cys) variant causes a missense change. The variant allele was found at a frequency of 0.113 in 1,611,568 control chromosomes in the GnomAD database, including 17,915 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_021176.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
G6PC2 | NM_021176.3 | c.1025C>G | p.Ser342Cys | missense_variant | 5/5 | ENST00000375363.8 | |
G6PC2 | XM_011511564.4 | c.797C>G | p.Ser266Cys | missense_variant | 3/3 | ||
G6PC2 | XM_011511565.4 | c.677C>G | p.Ser226Cys | missense_variant | 4/4 | ||
G6PC2 | NM_001081686.2 | c.*444C>G | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G6PC2 | ENST00000375363.8 | c.1025C>G | p.Ser342Cys | missense_variant | 5/5 | 1 | NM_021176.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.213 AC: 32369AN: 151966Hom.: 6300 Cov.: 32
GnomAD3 exomes AF: 0.117 AC: 29449AN: 251196Hom.: 3441 AF XY: 0.105 AC XY: 14223AN XY: 135794
GnomAD4 exome AF: 0.103 AC: 150363AN: 1459484Hom.: 11592 Cov.: 31 AF XY: 0.0988 AC XY: 71716AN XY: 726154
GnomAD4 genome ? AF: 0.213 AC: 32440AN: 152084Hom.: 6323 Cov.: 32 AF XY: 0.205 AC XY: 15234AN XY: 74352
ClinVar
Submissions by phenotype
G6PC2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 24, 2019 | This variant is classified as 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