11-7696766-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198185.7(OVCH2):c.959G>A(p.Gly320Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000633 in 1,611,632 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G320R) has been classified as Uncertain significance.
Frequency
Consequence
NM_198185.7 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OVCH2 | NM_198185.7 | c.959G>A | p.Gly320Glu | missense_variant | Exon 9 of 16 | ENST00000533663.6 | NP_937828.3 | |
OVCH2 | XM_047426878.1 | c.971G>A | p.Gly324Glu | missense_variant | Exon 9 of 18 | XP_047282834.1 | ||
LOC105376533 | XR_007062576.1 | n.954-2847C>T | intron_variant | Intron 4 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OVCH2 | ENST00000533663.6 | c.959G>A | p.Gly320Glu | missense_variant | Exon 9 of 16 | 5 | NM_198185.7 | ENSP00000484497.2 | ||
OVCH2 | ENST00000612000.1 | c.959G>A | p.Gly320Glu | missense_variant | Exon 9 of 15 | 5 | ENSP00000484790.1 | |||
OVCH2 | ENST00000673880.1 | c.836-1578G>A | intron_variant | Intron 7 of 11 | ENSP00000501258.1 | |||||
OVCH2 | ENST00000534817.1 | n.200G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000452 AC: 11AN: 243554Hom.: 0 AF XY: 0.0000379 AC XY: 5AN XY: 131920
GnomAD4 exome AF: 0.0000617 AC: 90AN: 1459356Hom.: 0 Cov.: 31 AF XY: 0.0000648 AC XY: 47AN XY: 725664
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.959G>A (p.G320E) alteration is located in exon 9 (coding exon 9) of the OVCH2 gene. This alteration results from a G to A substitution at nucleotide position 959, causing the glycine (G) at amino acid position 320 to be replaced by a glutamic acid (E). 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