12-29445388-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001353179.2(OVCH1):c.2876G>A(p.Arg959Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001353179.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OVCH1 | NM_001353179.2 | c.2876G>A | p.Arg959Lys | missense_variant | 23/26 | ENST00000537054.2 | NP_001340108.1 | |
OVCH1-AS1 | NR_073172.1 | n.561-41498C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OVCH1 | ENST00000537054.2 | c.2876G>A | p.Arg959Lys | missense_variant | 23/26 | 3 | NM_001353179.2 | ENSP00000445480 | P1 | |
OVCH1-AS1 | ENST00000551108.2 | n.561-41498C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457164Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 724894
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | The c.2771G>A (p.R924K) alteration is located in exon 23 (coding exon 23) of the OVCH1 gene. This alteration results from a G to A substitution at nucleotide position 2771, causing the arginine (R) at amino acid position 924 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