2-168907710-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_021176.3(G6PC2):c.699G>A(p.Leu233Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00157 in 1,614,102 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_021176.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
G6PC2 | NM_021176.3 | c.699G>A | p.Leu233Leu | synonymous_variant | Exon 5 of 5 | ENST00000375363.8 | NP_066999.1 | |
G6PC2 | XM_011511564.4 | c.471G>A | p.Leu157Leu | synonymous_variant | Exon 3 of 3 | XP_011509866.1 | ||
G6PC2 | XM_011511565.4 | c.351G>A | p.Leu117Leu | synonymous_variant | Exon 4 of 4 | XP_011509867.1 | ||
G6PC2 | NM_001081686.2 | c.*118G>A | 3_prime_UTR_variant | Exon 4 of 4 | NP_001075155.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00143 AC: 217AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00117 AC: 293AN: 251486Hom.: 1 AF XY: 0.00129 AC XY: 175AN XY: 135916
GnomAD4 exome AF: 0.00159 AC: 2319AN: 1461860Hom.: 2 Cov.: 33 AF XY: 0.00153 AC XY: 1113AN XY: 727232
GnomAD4 genome AF: 0.00144 AC: 219AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.00116 AC XY: 86AN XY: 74436
ClinVar
Submissions by phenotype
G6PC2-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