rs145731647
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_152783.5(D2HGDH):c.293-23A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000048 in 1,458,674 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 Pathogenic (no stars). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_152783.5 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
D2HGDH | NM_152783.5 | c.293-23A>G | intron_variant | ENST00000321264.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
D2HGDH | ENST00000321264.9 | c.293-23A>G | intron_variant | 1 | NM_152783.5 | P1 | |||
D2HGDH | ENST00000436747.5 | c.293-23A>G | intron_variant, NMD_transcript_variant | 1 | |||||
D2HGDH | ENST00000403782.5 | c.-110-23A>G | intron_variant | 2 | |||||
D2HGDH | ENST00000400769.6 | c.293-23A>G | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249638Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135082
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1458674Hom.: 0 Cov.: 29 AF XY: 0.00000551 AC XY: 4AN XY: 725794
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
D-2-hydroxyglutaric aciduria 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2005 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at