chr16-72012054-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001361.5(DHODH):c.26G>A(p.Arg9Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,613,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001361.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DHODH | NM_001361.5 | c.26G>A | p.Arg9Gln | missense_variant | 2/9 | ENST00000219240.9 | |
DHODH | XM_047433674.1 | c.-59G>A | 5_prime_UTR_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHODH | ENST00000219240.9 | c.26G>A | p.Arg9Gln | missense_variant | 2/9 | 1 | NM_001361.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000561 AC: 14AN: 249378Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135302
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461688Hom.: 0 Cov.: 32 AF XY: 0.0000426 AC XY: 31AN XY: 727156
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74452
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 24, 2021 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 9 of the DHODH protein (p.Arg9Gln). This variant is present in population databases (rs201486372, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with DHODH-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at