chr19-48936037-G-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_014475.4(DHDH):c.208G>T(p.Ala70Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DHDH
NM_014475.4 missense
NM_014475.4 missense
Scores
4
14
Clinical Significance
Conservation
PhyloP100: 4.11
Publications
0 publications found
Genes affected
DHDH (HGNC:17887): (dihydrodiol dehydrogenase) This gene encodes an enzyme that belongs to the family of dihydrodiol dehydrogenases, which exist in multiple forms in mammalian tissues and are involved in the metabolism of xenobiotics and sugars. These enzymes catalyze the NADP1-linked oxidation of transdihydrodiols of aromatic hydrocarbons to corresponding catechols. This enzyme is a dimeric dihydrodiol dehydrogenase, and it differs from monomeric dihydrodiol dehydrogenases in its high substrate specificity for trans-dihydrodiols of aromatic hydrocarbons in the oxidative direction. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014475.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DHDH | TSL:1 MANE Select | c.208G>T | p.Ala70Ser | missense | Exon 3 of 7 | ENSP00000221403.2 | Q9UQ10 | ||
| DHDH | TSL:5 | c.208G>T | p.Ala70Ser | missense | Exon 3 of 5 | ENSP00000428672.1 | E5RGT8 | ||
| DHDH | TSL:5 | c.202+926G>T | intron | N/A | ENSP00000428935.1 | E5RFE0 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1447724Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 718976
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1447724
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
718976
African (AFR)
AF:
AC:
0
AN:
33264
American (AMR)
AF:
AC:
0
AN:
42354
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25762
East Asian (EAS)
AF:
AC:
0
AN:
39150
South Asian (SAS)
AF:
AC:
0
AN:
83792
European-Finnish (FIN)
AF:
AC:
0
AN:
51750
Middle Eastern (MID)
AF:
AC:
0
AN:
5302
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1106528
Other (OTH)
AF:
AC:
0
AN:
59822
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
B
Vest4
MutPred
Gain of disorder (P = 0.0488)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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