16-72008926-T-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001361.5(DHODH):c.21+141T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 1,529,302 control chromosomes in the GnomAD database, including 462,451 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.82 ( 51859 hom., cov: 31)
Exomes 𝑓: 0.77 ( 410592 hom. )
Consequence
DHODH
NM_001361.5 intron
NM_001361.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.723
Genes affected
DHODH (HGNC:2867): (dihydroorotate dehydrogenase (quinone)) The protein encoded by this gene catalyzes the fourth enzymatic step, the ubiquinone-mediated oxidation of dihydroorotate to orotate, in de novo pyrimidine biosynthesis. This protein is a mitochondrial protein located on the outer surface of the inner mitochondrial membrane. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 16-72008926-T-G is Benign according to our data. Variant chr16-72008926-T-G is described in ClinVar as [Benign]. Clinvar id is 1229459.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DHODH | NM_001361.5 | c.21+141T>G | intron_variant | ENST00000219240.9 | |||
DHODH | XM_047433674.1 | c.-64+17T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHODH | ENST00000219240.9 | c.21+141T>G | intron_variant | 1 | NM_001361.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.821 AC: 124747AN: 151942Hom.: 51799 Cov.: 31
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GnomAD4 exome AF: 0.770 AC: 1060869AN: 1377242Hom.: 410592 Cov.: 51 AF XY: 0.770 AC XY: 521154AN XY: 677030
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GnomAD4 genome AF: 0.821 AC: 124868AN: 152060Hom.: 51859 Cov.: 31 AF XY: 0.820 AC XY: 60968AN XY: 74312
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 16, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at