Variant rs1154470 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_000673.7(ADH7):c.18+36C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 1,604,726 control chromosomes in the GnomAD database, including 87,217 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 0.28 ( 6558 hom., cov: 32)

Exomes 𝑓: 0.33 ( 80659 hom. )

Consequence

ADH7
NM_000673.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADH7	NM_000673.7 linkuse as main transcript	c.18+36C>T		intron_variant		ENST00000437033.7	NP_000664.3
ADH7	NM_001166504.2 linkuse as main transcript			upstream_gene_variant			NP_001159976.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
ADH7	ENST00000437033.7 linkuse as main transcript	c.18+36C>T	intron_variant	1	NM_000673.7	ENSP00000414254	P1
ADH7	ENST00000209665.8 linkuse as main transcript	c.54+36C>T	intron_variant	1		ENSP00000209665		P40394-1
ADH7	ENST00000482593.5 linkuse as main transcript	c.-267+36C>T	intron_variant	3		ENSP00000420613
ADH7	ENST00000476959.5 linkuse as main transcript		upstream_gene_variant	2		ENSP00000420269		P40394-2

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

41995

AN:

151880

Hom.:

6550

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.368

Gnomad ASJ

AF:

0.243

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.356

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.277

GnomAD3 exomes

AF:

0.325

AC:

78158

AN:

240378

Hom.:

13245

AF XY:

0.323

AC XY:

41945

AN XY:

129746

show subpopulations

Gnomad AFR exome

AF:

0.120

Gnomad AMR exome

AF:

0.463

Gnomad ASJ exome

AF:

0.237

Gnomad EAS exome

AF:

0.258

Gnomad SAS exome

AF:

0.297

Gnomad FIN exome

AF:

0.352

Gnomad NFE exome

AF:

0.333

Gnomad OTH exome

AF:

0.339

GnomAD4 exome

AF:

0.329

AC:

478122

AN:

1452730

Hom.:

80659

Cov.:

AF XY:

0.328

AC XY:

236572

AN XY:

722200

show subpopulations

Gnomad4 AFR exome

AF:

0.114

Gnomad4 AMR exome

AF:

0.447

Gnomad4 ASJ exome

AF:

0.239

Gnomad4 EAS exome

AF:

0.246

Gnomad4 SAS exome

AF:

0.299

Gnomad4 FIN exome

AF:

0.353

Gnomad4 NFE exome

AF:

0.338

Gnomad4 OTH exome

AF:

0.328

GnomAD4 genome

AF:

0.276

AC:

42019

AN:

151996

Hom.:

6558

Cov.:

AF XY:

0.281

AC XY:

20888

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.131

Gnomad4 AMR

AF:

0.368

Gnomad4 ASJ

AF:

0.243

Gnomad4 EAS

AF:

0.269

Gnomad4 SAS

AF:

0.307

Gnomad4 FIN

AF:

0.356

Gnomad4 NFE

AF:

0.331

Gnomad4 OTH

AF:

0.277

Alfa

AF:

0.302

Hom.:

1938

Bravo

AF:

0.274

Asia WGS

AF:

0.316

AC:

1101

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.38

DANN

Benign

0.22

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

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