12-29444161-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001353179.2(OVCH1):c.3106C>T(p.His1036Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000056 in 1,607,290 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OVCH1 | NM_001353179.2 | c.3106C>T | p.His1036Tyr | missense_variant | 24/26 | ENST00000537054.2 | NP_001340108.1 | |
OVCH1-AS1 | NR_073172.1 | n.561-42725G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OVCH1 | ENST00000537054.2 | c.3106C>T | p.His1036Tyr | missense_variant | 24/26 | 3 | NM_001353179.2 | ENSP00000445480 | P1 | |
OVCH1-AS1 | ENST00000551108.2 | n.561-42725G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152002Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 243392Hom.: 0 AF XY: 0.0000227 AC XY: 3AN XY: 132050
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1455288Hom.: 0 Cov.: 30 AF XY: 0.00000553 AC XY: 4AN XY: 723796
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74242
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 27, 2023 | The c.3001C>T (p.H1001Y) alteration is located in exon 24 (coding exon 24) of the OVCH1 gene. This alteration results from a C to T substitution at nucleotide position 3001, causing the histidine (H) at amino acid position 1001 to be replaced by a tyrosine (Y). 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