chr2-241735230-G-GC
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_152783.5(D2HGDH):c.10dup(p.Arg4ProfsTer61) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000735 in 1,360,366 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. L2L) has been classified as Likely benign.
Frequency
Consequence
NM_152783.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
D2HGDH | NM_152783.5 | c.10dup | p.Arg4ProfsTer61 | frameshift_variant | 2/10 | ENST00000321264.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
D2HGDH | ENST00000321264.9 | c.10dup | p.Arg4ProfsTer61 | frameshift_variant | 2/10 | 1 | NM_152783.5 | P1 | |
ENST00000400768.2 | n.268_269insG | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 7.35e-7 AC: 1AN: 1360366Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 671430
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
D-2-hydroxyglutaric aciduria 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at