2-168908036-C-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The ENST00000375363.8(G6PC2):āc.1025C>Gā(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 (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000375363.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
G6PC2 | NM_021176.3 | c.1025C>G | p.Ser342Cys | missense_variant | 5/5 | ENST00000375363.8 | NP_066999.1 | |
G6PC2 | XM_011511564.4 | c.797C>G | p.Ser266Cys | missense_variant | 3/3 | XP_011509866.1 | ||
G6PC2 | XM_011511565.4 | c.677C>G | p.Ser226Cys | missense_variant | 4/4 | XP_011509867.1 | ||
G6PC2 | NM_001081686.2 | c.*444C>G | 3_prime_UTR_variant | 4/4 | NP_001075155.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
G6PC2 | ENST00000375363.8 | c.1025C>G | p.Ser342Cys | missense_variant | 5/5 | 1 | NM_021176.3 | ENSP00000364512 | 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, no assertion criteria provided | 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