chr10-49739708-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_018245.3(OGDHL):c.2272C>T(p.Arg758Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000316 in 1,613,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R758Q) has been classified 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 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OGDHL | NM_018245.3 | c.2272C>T | p.Arg758Trp | missense_variant | 17/23 | ENST00000374103.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OGDHL | ENST00000374103.9 | c.2272C>T | p.Arg758Trp | missense_variant | 17/23 | 1 | NM_018245.3 | P1 | |
OGDHL | ENST00000419399.4 | c.2101C>T | p.Arg701Trp | missense_variant | 16/22 | 2 | |||
OGDHL | ENST00000432695.2 | c.1645C>T | p.Arg549Trp | missense_variant | 15/21 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251124Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135700
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461740Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 727184
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.2272C>T (p.R758W) alteration is located in exon 17 (coding exon 16) of the OGDHL gene. This alteration results from a C to T substitution at nucleotide position 2272, causing the arginine (R) at amino acid position 758 to be replaced by a tryptophan (W). 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