2-168907957-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000375363.8(G6PC2):c.946G>A(p.Glu316Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,614,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000375363.8 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
G6PC2 | NM_021176.3 | c.946G>A | p.Glu316Lys | missense_variant | 5/5 | ENST00000375363.8 | NP_066999.1 | |
G6PC2 | XM_011511564.4 | c.718G>A | p.Glu240Lys | missense_variant | 3/3 | XP_011509866.1 | ||
G6PC2 | XM_011511565.4 | c.598G>A | p.Glu200Lys | missense_variant | 4/4 | XP_011509867.1 | ||
G6PC2 | NM_001081686.2 | c.*365G>A | 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.946G>A | p.Glu316Lys | missense_variant | 5/5 | 1 | NM_021176.3 | ENSP00000364512 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251484Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135916
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461790Hom.: 0 Cov.: 33 AF XY: 0.0000371 AC XY: 27AN XY: 727204
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 08, 2022 | The c.946G>A (p.E316K) alteration is located in exon 5 (coding exon 5) of the G6PC2 gene. This alteration results from a G to A substitution at nucleotide position 946, causing the glutamic acid (E) at amino acid position 316 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at