Variant chr4-99207596-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001102470.2(ADH6):c.829-15A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 1,610,410 control chromosomes in the GnomAD database, including 120,390 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 0.43 ( 15308 hom., cov: 32)

Exomes 𝑓: 0.36 ( 105082 hom. )

Consequence

ADH6
NM_001102470.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32

Variant links:

Genes affected

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:

ENSG00000246090 (HGNC:):

ENSG00000246090 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
ADH6	NM_001102470.2 link	c.829-15A>G	intron_variant	ENST00000394899.6	NP_001095940.1	P28332-2Q8IUN7
ADH6	NM_000672.4 link	c.829-15A>G	intron_variant		NP_000663.1	P28332-1Q8IUN7
LOC100507053	NR_037884.1 link	n.3789+3165T>C	intron_variant
ADH6	NR_132990.2 link	n.564-15A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADH6	ENST00000394899.6 link	c.829-15A>G		intron_variant		2	NM_001102470.2	ENSP00000378359.2		P28332-2

Frequencies

GnomAD3 genomes

AF:

0.429

AC:

65154

AN:

151828

Hom.:

15295

Cov.:

show subpopulations

Gnomad AFR

AF:

0.559

Gnomad AMI

AF:

0.317

Gnomad AMR

AF:

0.465

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.876

Gnomad SAS

AF:

0.480

Gnomad FIN

AF:

0.298

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.411

GnomAD3 exomes

AF:

0.427

AC:

106112

AN:

248636

Hom.:

25524

AF XY:

0.419

AC XY:

56217

AN XY:

134320

show subpopulations

Gnomad AFR exome

AF:

0.566

Gnomad AMR exome

AF:

0.503

Gnomad ASJ exome

AF:

0.342

Gnomad EAS exome

AF:

0.886

Gnomad SAS exome

AF:

0.436

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.341

Gnomad OTH exome

AF:

0.378

GnomAD4 exome

AF:

0.363

AC:

529539

AN:

1458464

Hom.:

105082

Cov.:

AF XY:

0.365

AC XY:

264947

AN XY:

725524

show subpopulations

Gnomad4 AFR exome

AF:

0.568

Gnomad4 AMR exome

AF:

0.497

Gnomad4 ASJ exome

AF:

0.339

Gnomad4 EAS exome

AF:

0.890

Gnomad4 SAS exome

AF:

0.443

Gnomad4 FIN exome

AF:

0.297

Gnomad4 NFE exome

AF:

0.330

Gnomad4 OTH exome

AF:

0.378

GnomAD4 genome

AF:

0.429

AC:

65209

AN:

151946

Hom.:

15308

Cov.:

AF XY:

0.432

AC XY:

32086

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.559

Gnomad4 AMR

AF:

0.465

Gnomad4 ASJ

AF:

0.347

Gnomad4 EAS

AF:

0.877

Gnomad4 SAS

AF:

0.480

Gnomad4 FIN

AF:

0.298

Gnomad4 NFE

AF:

0.331

Gnomad4 OTH

AF:

0.410

Alfa

AF:

0.362

Hom.:

14025

Bravo

AF:

0.450

Asia WGS

AF:

0.580

AC:

2013

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.63

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over