dbSNP rs284786: ADH7:c.*328A>T (chr4-99412820-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000673.7(ADH7):c.*328A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 247,996 control chromosomes in the GnomAD database, including 17,137 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.36 ( 10968 hom., cov: 33)

Exomes 𝑓: 0.33 ( 6169 hom. )

Consequence

ADH7
NM_000673.7 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65

Publications

14 publications found

Variant links:

Genes affected

ADH7 (HGNC:256): (alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide) This gene encodes class IV alcohol dehydrogenase 7 mu or sigma subunit, which is a member of the alcohol dehydrogenase family. Members of this family metabolize a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. The enzyme encoded by this gene is inefficient in ethanol oxidation, but is the most active as a retinol dehydrogenase; thus it may participate in the synthesis of retinoic acid, a hormone important for cellular differentiation. The expression of this gene is much more abundant in stomach than liver, thus differing from the other known gene family members. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

ADH7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADH7	NM_000673.7 link	c.*328A>T		3_prime_UTR_variant	Exon 9 of 9	ENST00000437033.7	NP_000664.3	P40394
ADH7	NM_001166504.2 link	c.*328A>T		3_prime_UTR_variant	Exon 9 of 9		NP_001159976.1	P40394-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADH7	ENST00000437033.7 link	c.*328A>T		3_prime_UTR_variant	Exon 9 of 9	1	NM_000673.7	ENSP00000414254.2		A0A0C4DG85

Frequencies

GnomAD3 genomes

AF:

0.363

AC:

55137

AN:

151942

Hom.:

10961

Cov.:

show subpopulations

Gnomad AFR

AF:

0.513

Gnomad AMI

AF:

0.306

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.590

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.335

GnomAD4 exome

AF:

0.331

AC:

31728

AN:

95936

Hom.:

6169

Cov.:

AF XY:

0.333

AC XY:

16615

AN XY:

49862

show subpopulations

African (AFR)

AF:

0.493

AC:

1398

AN:

2838

American (AMR)

AF:

0.289

AC:

1148

AN:

3966

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

822

AN:

3324

East Asian (EAS)

AF:

0.721

AC:

4710

AN:

6530

South Asian (SAS)

AF:

0.433

AC:

2092

AN:

4830

European-Finnish (FIN)

AF:

0.191

AC:

958

AN:

5014

Middle Eastern (MID)

AF:

0.369

AC:

167

AN:

452

European-Non Finnish (NFE)

AF:

0.295

AC:

18515

AN:

62800

Other (OTH)

AF:

0.310

AC:

1918

AN:

6182

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

980

1960

2939

3919

4899

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

122

244

366

488

610

<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:

0.363

AC:

55183

AN:

152060

Hom.:

10968

Cov.:

AF XY:

0.362

AC XY:

26917

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.512

AC:

21244

AN:

41464

American (AMR)

AF:

0.298

AC:

4547

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.267

AC:

928

AN:

3470

East Asian (EAS)

AF:

0.590

AC:

3057

AN:

5184

South Asian (SAS)

AF:

0.454

AC:

2190

AN:

4822

European-Finnish (FIN)

AF:

0.189

AC:

2003

AN:

10586

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.296

AC:

20109

AN:

67942

Other (OTH)

AF:

0.336

AC:

708

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1721

3443

5164

6886

8607

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.187

Hom.:

370

Bravo

AF:

0.378

Asia WGS

AF:

0.424

AC:

1467

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.33

(source)

DANN

Benign

0.34

PhyloP100

-1.6

Mutation Taster

=100/0

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