dbSNP rs3805331: ADH7:c.*373T>C (chr4-99412775-A-G) – 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.*373T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0615 in 173,784 control chromosomes in the GnomAD database, including 347 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 0.061 ( 304 hom., cov: 33)

Exomes 𝑓: 0.065 ( 43 hom. )

Consequence

ADH7
NM_000673.7 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.440

Publications

8 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:

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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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADH7	NM_000673.7 link	c.*373T>C		3_prime_UTR_variant	Exon 9 of 9	ENST00000437033.7	NP_000664.3	P40394
ADH7	NM_001166504.2 link	c.*373T>C		3_prime_UTR_variant	Exon 9 of 9		NP_001159976.1	P40394-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ADH7	ENST00000437033.7 link	c.*373T>C	3_prime_UTR_variant	Exon 9 of 9	1	NM_000673.7	ENSP00000414254.2	A0A0C4DG85
ADH7	ENST00000209665.8 link	c.*373T>C	3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000209665.4	P40394-1
ADH7	ENST00000482593.5 link	c.*373T>C	downstream_gene_variant		3		ENSP00000420613.1	E9PFG0
ADH7	ENST00000485660.1 link	n.*239T>C	downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0611

AC:

9298

AN:

152134

Hom.:

305

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0519

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0612

Gnomad ASJ

AF:

0.0620

Gnomad EAS

AF:

0.0749

Gnomad SAS

AF:

0.0995

Gnomad FIN

AF:

0.0563

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0641

Gnomad OTH

AF:

0.0593

GnomAD4 exome

AF:

0.0645

AC:

1389

AN:

21530

Hom.:

Cov.:

AF XY:

0.0641

AC XY:

715

AN XY:

11158

show subpopulations

African (AFR)

AF:

0.0392

AC:

AN:

790

American (AMR)

AF:

0.0753

AC:

AN:

810

Ashkenazi Jewish (ASJ)

AF:

0.0508

AC:

AN:

788

East Asian (EAS)

AF:

0.0625

AC:

AN:

1424

South Asian (SAS)

AF:

0.0836

AC:

AN:

538

European-Finnish (FIN)

AF:

0.0493

AC:

AN:

812

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

126

European-Non Finnish (NFE)

AF:

0.0666

AC:

986

AN:

14804

Other (OTH)

AF:

0.0633

AC:

AN:

1438

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

118

178

237

296

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0611

AC:

9301

AN:

152254

Hom.:

304

Cov.:

AF XY:

0.0609

AC XY:

4531

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.0519

AC:

2157

AN:

41570

American (AMR)

AF:

0.0612

AC:

936

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0620

AC:

215

AN:

3468

East Asian (EAS)

AF:

0.0744

AC:

386

AN:

5186

South Asian (SAS)

AF:

0.0988

AC:

476

AN:

4820

European-Finnish (FIN)

AF:

0.0563

AC:

597

AN:

10604

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0642

AC:

4362

AN:

67990

Other (OTH)

AF:

0.0610

AC:

129

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

453

905

1358

1810

2263

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0619

Hom.:

432

Bravo

AF:

0.0602

Asia WGS

AF:

0.110

AC:

379

AN:

3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.9

(source)

DANN

Benign

0.69

PhyloP100

0.44

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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rs3805331

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