Genetic Variant ENSG00000246090:n.3715-1738C>A (chr4-99202619-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000500358.6(ENSG00000246090):n.3715-1738C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 396,300 control chromosomes in the GnomAD database, including 63,587 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 0.56 ( 24730 hom., cov: 32)

Exomes 𝑓: 0.55 ( 38857 hom. )

Consequence

ENSG00000246090
ENST00000500358.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.398

Publications

7 publications found

Variant links:

Genes affected

ENSG00000246090 (HGNC:):

ENSG00000246090 links:

ADH6 (HGNC:255): (alcohol dehydrogenase 6 (class V)) This gene encodes class V alcohol dehydrogenase, 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. This gene is expressed in the stomach as well as in the liver, and it contains a glucocorticoid response element upstream of its 5' UTR, which is a steroid hormone receptor binding site. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ADH6 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1 link	n.3715-1738C>A	intron_variant	Intron 3 of 9
ADH6	NM_001102470.2 link	c.*1600G>T	downstream_gene_variant		ENST00000394899.6	NP_001095940.1	P28332-2Q8IUN7
ADH6	NM_000672.4 link	c.*2302G>T	downstream_gene_variant			NP_000663.1	P28332-1Q8IUN7
ADH6	NR_132990.2 link	n.*20G>T	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADH6	ENST00000394899.6 link	c.*1600G>T		downstream_gene_variant		2	NM_001102470.2	ENSP00000378359.2		P28332-2

Frequencies

GnomAD3 genomes

AF:

0.563

AC:

85451

AN:

151868

Hom.:

24707

Cov.:

show subpopulations

Gnomad AFR

AF:

0.642

Gnomad AMI

AF:

0.582

Gnomad AMR

AF:

0.599

Gnomad ASJ

AF:

0.571

Gnomad EAS

AF:

0.879

Gnomad SAS

AF:

0.561

Gnomad FIN

AF:

0.465

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.497

Gnomad OTH

AF:

0.568

GnomAD4 exome

AF:

0.549

AC:

134226

AN:

244316

Hom.:

38857

Cov.:

AF XY:

0.549

AC XY:

67969

AN XY:

123882

show subpopulations

African (AFR)

AF:

0.650

AC:

4623

AN:

7112

American (AMR)

AF:

0.587

AC:

4344

AN:

7402

Ashkenazi Jewish (ASJ)

AF:

0.574

AC:

5258

AN:

9156

East Asian (EAS)

AF:

0.895

AC:

20461

AN:

22870

South Asian (SAS)

AF:

0.535

AC:

1501

AN:

2806

European-Finnish (FIN)

AF:

0.468

AC:

9699

AN:

20736

Middle Eastern (MID)

AF:

0.502

AC:

640

AN:

1276

European-Non Finnish (NFE)

AF:

0.503

AC:

78781

AN:

156690

Other (OTH)

AF:

0.548

AC:

8919

AN:

16268

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

2805

5610

8416

11221

14026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

362

724

1086

1448

1810

<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:

0.563

AC:

85521

AN:

151984

Hom.:

24730

Cov.:

AF XY:

0.562

AC XY:

41785

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.642

AC:

26625

AN:

41444

American (AMR)

AF:

0.599

AC:

9145

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.571

AC:

1983

AN:

3470

East Asian (EAS)

AF:

0.879

AC:

4547

AN:

5172

South Asian (SAS)

AF:

0.560

AC:

2701

AN:

4820

European-Finnish (FIN)

AF:

0.465

AC:

4915

AN:

10564

Middle Eastern (MID)

AF:

0.510

AC:

150

AN:

294

European-Non Finnish (NFE)

AF:

0.497

AC:

33728

AN:

67926

Other (OTH)

AF:

0.566

AC:

1196

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1917

3834

5752

7669

9586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

724

1448

2172

2896

3620

<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:

0.527

Hom.:

83184

Bravo

AF:

0.578

Asia WGS

AF:

0.629

AC:

2187

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.67

(source)

DANN

Benign

0.70

PhyloP100

-0.40

Splicing

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