dbSNP rs3835153: DHDH:p.Glu294ValfsTer18 (chr19-48944491-GGA-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_014475.4(DHDH):c.881_882delAG(p.Glu294ValfsTer18) variant causes a frameshift change. The variant allele was found at a frequency of 0.0755 in 1,608,572 control chromosomes in the GnomAD database, including 5,474 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.066 ( 526 hom., cov: 31)

Exomes 𝑓: 0.076 ( 4948 hom. )

Consequence

DHDH
NM_014475.4 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.69

Publications

10 publications found

Variant links:

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]

DHDH links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.077 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DHDH	NM_014475.4 link	c.881_882delAG	p.Glu294ValfsTer18	frameshift_variant	Exon 6 of 7	ENST00000221403.7	NP_055290.1	Q9UQ10
DHDH	XM_017026598.2 link	c.632_633delAG	p.Glu211ValfsTer18	frameshift_variant	Exon 6 of 7		XP_016882087.1
DHDH	XM_005258748.5 link	c.545_546delAG	p.Glu182ValfsTer18	frameshift_variant	Exon 5 of 6		XP_005258805.1
DHDH	XM_047438617.1 link	c.84_85delAG		3_prime_UTR_variant	Exon 5 of 5		XP_047294573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DHDH	ENST00000221403.7 link	c.881_882delAG	p.Glu294ValfsTer18	frameshift_variant	Exon 6 of 7	1	NM_014475.4	ENSP00000221403.2		Q9UQ10

Frequencies

GnomAD3 genomes

AF:

0.0662

AC:

10062

AN:

152076

Hom.:

524

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0128

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.0719

Gnomad ASJ

AF:

0.0164

Gnomad EAS

AF:

0.0469

Gnomad SAS

AF:

0.0629

Gnomad FIN

AF:

0.217

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0787

Gnomad OTH

AF:

0.0578

GnomAD2 exomes

AF:

0.0769

AC:

19128

AN:

248690

AF XY:

0.0767

show subpopulations

Gnomad AFR exome

AF:

0.0115

Gnomad AMR exome

AF:

0.0748

Gnomad ASJ exome

AF:

0.0191

Gnomad EAS exome

AF:

0.0474

Gnomad FIN exome

AF:

0.208

Gnomad NFE exome

AF:

0.0774

Gnomad OTH exome

AF:

0.0691

GnomAD4 exome

AF:

0.0765

AC:

111343

AN:

1456378

Hom.:

4948

AF XY:

0.0756

AC XY:

54677

AN XY:

723556

show subpopulations

African (AFR)

AF:

0.0110

AC:

369

AN:

33400

American (AMR)

AF:

0.0771

AC:

3428

AN:

44444

Ashkenazi Jewish (ASJ)

AF:

0.0163

AC:

423

AN:

25904

East Asian (EAS)

AF:

0.0463

AC:

1831

AN:

39556

South Asian (SAS)

AF:

0.0558

AC:

4792

AN:

85846

European-Finnish (FIN)

AF:

0.201

AC:

10739

AN:

53302

Middle Eastern (MID)

AF:

0.0271

AC:

156

AN:

5758

European-Non Finnish (NFE)

AF:

0.0773

AC:

85599

AN:

1108052

Other (OTH)

AF:

0.0666

AC:

4006

AN:

60116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

5923

11846

17768

23691

29614

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3112

6224

9336

12448

15560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0661

AC:

10063

AN:

152194

Hom.:

526

Cov.:

AF XY:

0.0726

AC XY:

5399

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.0128

AC:

532

AN:

41538

American (AMR)

AF:

0.0721

AC:

1101

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0164

AC:

AN:

3470

East Asian (EAS)

AF:

0.0468

AC:

243

AN:

5188

South Asian (SAS)

AF:

0.0630

AC:

304

AN:

4826

European-Finnish (FIN)

AF:

0.217

AC:

2300

AN:

10584

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0787

AC:

5354

AN:

67996

Other (OTH)

AF:

0.0568

AC:

120

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

466

932

1398

1864

2330

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0196

Hom.:

178

Bravo

AF:

0.0525

Asia WGS

AF:

0.0590

AC:

204

AN:

3478

EpiCase

AF:

0.0693

EpiControl

AF:

0.0661

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.7

Mutation Taster

=117/83

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over