7-44624382-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002541.4(OGDH):āc.39A>Gā(p.Pro13Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000805 in 1,602,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. P13P) has been classified as Benign.
Frequency
Consequence
NM_002541.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OGDH | NM_002541.4 | c.39A>G | p.Pro13Pro | synonymous_variant | 2/23 | ENST00000222673.6 | NP_002532.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OGDH | ENST00000222673.6 | c.39A>G | p.Pro13Pro | synonymous_variant | 2/23 | 1 | NM_002541.4 | ENSP00000222673.5 |
Frequencies
GnomAD3 genomes AF: 0.0000280 AC: 4AN: 142848Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251478Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135910
GnomAD4 exome AF: 0.0000856 AC: 125AN: 1459500Hom.: 0 Cov.: 36 AF XY: 0.0000730 AC XY: 53AN XY: 726078
GnomAD4 genome AF: 0.0000280 AC: 4AN: 142848Hom.: 0 Cov.: 30 AF XY: 0.0000146 AC XY: 1AN XY: 68488
ClinVar
Submissions by phenotype
Oxoglutaricaciduria Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 31, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at