dbSNP rs894369: ADH7:c.*459G>C (chr4-99412689-C-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.*459G>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 0.775 in 152,378 control chromosomes in the GnomAD database, including 46,285 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 0.78 ( 46183 hom., cov: 32)

Exomes 𝑓: 0.78 ( 102 hom. )

Consequence

ADH7
NM_000673.7 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.216

Publications

10 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADH7	NM_000673.7 link	c.*459G>C		3_prime_UTR_variant	Exon 9 of 9	ENST00000437033.7	NP_000664.3	P40394
ADH7	NM_001166504.2 link	c.*459G>C		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.*459G>C		3_prime_UTR_variant	Exon 9 of 9	1	NM_000673.7	ENSP00000414254.2		A0A0C4DG85
ADH7	ENST00000209665.8 link	c.*459G>C		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000209665.4		P40394-1

Frequencies

GnomAD3 genomes

AF:

0.775

AC:

117813

AN:

151926

Hom.:

46148

Cov.:

show subpopulations

Gnomad AFR

AF:

0.840

Gnomad AMI

AF:

0.774

Gnomad AMR

AF:

0.610

Gnomad ASJ

AF:

0.678

Gnomad EAS

AF:

0.650

Gnomad SAS

AF:

0.705

Gnomad FIN

AF:

0.770

Gnomad MID

AF:

0.728

Gnomad NFE

AF:

0.795

Gnomad OTH

AF:

0.731

GnomAD4 exome

AF:

0.778

AC:

260

AN:

334

Hom.:

102

Cov.:

AF XY:

0.766

AC XY:

144

AN XY:

188

show subpopulations

African (AFR)

AF:

0.900

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.667

AC:

AN:

East Asian (EAS)

AF:

0.833

AC:

AN:

South Asian (SAS)

AF:

0.850

AC:

AN:

European-Finnish (FIN)

AF:

0.786

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.777

AC:

185

AN:

238

Other (OTH)

AF:

0.875

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.775

AC:

117900

AN:

152044

Hom.:

46183

Cov.:

AF XY:

0.769

AC XY:

57159

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.840

AC:

34858

AN:

41484

American (AMR)

AF:

0.610

AC:

9306

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.678

AC:

2350

AN:

3468

East Asian (EAS)

AF:

0.650

AC:

3366

AN:

5178

South Asian (SAS)

AF:

0.706

AC:

3397

AN:

4814

European-Finnish (FIN)

AF:

0.770

AC:

8141

AN:

10574

Middle Eastern (MID)

AF:

0.721

AC:

212

AN:

294

European-Non Finnish (NFE)

AF:

0.795

AC:

54029

AN:

67948

Other (OTH)

AF:

0.727

AC:

1535

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1331

2662

3994

5325

6656

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

866

1732

2598

3464

4330

<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:

0.782

Hom.:

25584

Bravo

AF:

0.764

Asia WGS

AF:

0.602

AC:

2087

AN:

3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.7

(source)

DANN

Benign

0.79

PhyloP100

-0.22

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