10-49736038-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018245.3(OGDHL):c.2894G>A(p.Arg965His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000944 in 1,589,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018245.3 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 | UniProt |
---|---|---|---|---|---|---|---|
OGDHL | NM_018245.3 | c.2894G>A | p.Arg965His | missense_variant | 22/23 | ENST00000374103.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OGDHL | ENST00000374103.9 | c.2894G>A | p.Arg965His | missense_variant | 22/23 | 1 | NM_018245.3 | P1 | |
OGDHL | ENST00000419399.4 | c.2723G>A | p.Arg908His | missense_variant | 21/22 | 2 | |||
OGDHL | ENST00000432695.2 | c.2267G>A | p.Arg756His | missense_variant | 20/21 | 2 | |||
OGDHL | ENST00000490844.1 | n.1930G>A | non_coding_transcript_exon_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000132 AC: 3AN: 226782Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 121464
GnomAD4 exome AF: 0.00000905 AC: 13AN: 1437186Hom.: 0 Cov.: 34 AF XY: 0.00000841 AC XY: 6AN XY: 713014
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
OGDHL-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 30, 2022 | The OGDHL c.2894G>A variant is predicted to result in the amino acid substitution p.Arg965His. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0062% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/10-50944084-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at