Genetic Variant ENSG00000246090:n.3789+15235T>A (chr4-99219666-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 ENST00000500358.6(ENSG00000246090):n.3789+15235T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 153,236 control chromosomes in the GnomAD database, including 12,195 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 0.37 ( 12050 hom., cov: 32)

Exomes 𝑓: 0.45 ( 145 hom. )

Consequence

ENSG00000246090
ENST00000500358.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.594

Publications

5 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=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1 link	n.3789+15235T>A		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000246090	ENST00000500358.6 link	n.3789+15235T>A	intron_variant	Intron 4 of 9	1
ENSG00000246090	ENST00000506160.1 link	n.407+15235T>A	intron_variant	Intron 3 of 4	4
ENSG00000246090	ENST00000506454.2 link	n.168+15239T>A	intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.373

AC:

56617

AN:

151844

Hom.:

12048

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.509

Gnomad AMR

AF:

0.500

Gnomad ASJ

AF:

0.544

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.481

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.465

Gnomad OTH

AF:

0.427

GnomAD4 exome

AF:

0.447

AC:

569

AN:

1274

Hom.:

145

AF XY:

0.429

AC XY:

333

AN XY:

776

show subpopulations

African (AFR)

AF:

0.143

AC:

AN:

American (AMR)

AF:

0.583

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.615

AC:

AN:

East Asian (EAS)

AF:

0.219

AC:

AN:

South Asian (SAS)

AF:

0.292

AC:

AN:

European-Finnish (FIN)

AF:

0.583

AC:

AN:

Middle Eastern (MID)

AF:

0.167

AC:

AN:

European-Non Finnish (NFE)

AF:

0.453

AC:

467

AN:

1030

Other (OTH)

AF:

0.466

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.538

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.373

AC:

56650

AN:

151962

Hom.:

12050

Cov.:

AF XY:

0.371

AC XY:

27540

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.176

AC:

7291

AN:

41472

American (AMR)

AF:

0.500

AC:

7630

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.544

AC:

1888

AN:

3468

East Asian (EAS)

AF:

0.132

AC:

679

AN:

5154

South Asian (SAS)

AF:

0.218

AC:

1048

AN:

4816

European-Finnish (FIN)

AF:

0.481

AC:

5075

AN:

10554

Middle Eastern (MID)

AF:

0.397

AC:

116

AN:

292

European-Non Finnish (NFE)

AF:

0.465

AC:

31566

AN:

67946

Other (OTH)

AF:

0.425

AC:

894

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1636

3272

4909

6545

8181

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.411

Hom.:

1654

Bravo

AF:

0.369

Asia WGS

AF:

0.222

AC:

775

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.51

(source)

DANN

Benign

0.28

PhyloP100

-0.59

PromoterAI

0.017

Neutral

(source)

Splicing

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

Publications

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chr4-99219666-T-A

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