10-49735293-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018245.3(OGDHL):c.2968G>C(p.Val990Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,614,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OGDHL | NM_018245.3 | c.2968G>C | p.Val990Leu | missense_variant | 23/23 | ENST00000374103.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OGDHL | ENST00000374103.9 | c.2968G>C | p.Val990Leu | missense_variant | 23/23 | 1 | NM_018245.3 | P1 | |
OGDHL | ENST00000419399.4 | c.2797G>C | p.Val933Leu | missense_variant | 22/22 | 2 | |||
OGDHL | ENST00000432695.2 | c.2341G>C | p.Val781Leu | missense_variant | 21/21 | 2 | |||
OGDHL | ENST00000490844.1 | n.2004G>C | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000144 AC: 22AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251382Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135852
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461784Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727200
GnomAD4 genome ? AF: 0.000144 AC: 22AN: 152376Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74516
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 24, 2022 | The c.2968G>C (p.V990L) alteration is located in exon 23 (coding exon 22) of the OGDHL gene. This alteration results from a G to C substitution at nucleotide position 2968, causing the valine (V) at amino acid position 990 to be replaced by a leucine (L). 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