NM_018245.3:c.564C>T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_018245.3(OGDHL):c.564C>T(p.Leu188Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 1,613,382 control chromosomes in the GnomAD database, including 193,363 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_018245.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OGDHL | NM_018245.3 | c.564C>T | p.Leu188Leu | synonymous_variant | Exon 5 of 23 | ENST00000374103.9 | NP_060715.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OGDHL | ENST00000374103.9 | c.564C>T | p.Leu188Leu | synonymous_variant | Exon 5 of 23 | 1 | NM_018245.3 | ENSP00000363216.4 | ||
OGDHL | ENST00000419399.4 | c.393C>T | p.Leu131Leu | synonymous_variant | Exon 4 of 22 | 2 | ENSP00000401356.1 | |||
OGDHL | ENST00000432695.2 | c.-64C>T | 5_prime_UTR_variant | Exon 3 of 21 | 2 | ENSP00000390240.1 |
Frequencies
GnomAD3 genomes AF: 0.412 AC: 62596AN: 151936Hom.: 14876 Cov.: 32
GnomAD3 exomes AF: 0.489 AC: 122670AN: 251048Hom.: 32572 AF XY: 0.483 AC XY: 65599AN XY: 135692
GnomAD4 exome AF: 0.485 AC: 708694AN: 1461328Hom.: 178488 Cov.: 47 AF XY: 0.481 AC XY: 350030AN XY: 726986
GnomAD4 genome AF: 0.412 AC: 62608AN: 152054Hom.: 14875 Cov.: 32 AF XY: 0.415 AC XY: 30858AN XY: 74330
ClinVar
Submissions by phenotype
OGDHL-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at