Variant chr4-99420704-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_000673.7(ADH7):c.654G>A(p.Arg218=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,613,624 control chromosomes in the GnomAD database, including 11,731 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 0.13 ( 1435 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10296 hom. )

Consequence

ADH7
NM_000673.7 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.672

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BP7

Synonymous conserved (PhyloP=0.672 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADH7	NM_000673.7 linkuse as main transcript	c.654G>A	p.Arg218=	synonymous_variant	6/9	ENST00000437033.7
ADH7	NM_001166504.2 linkuse as main transcript	c.714G>A	p.Arg238=	synonymous_variant	6/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADH7	ENST00000437033.7 linkuse as main transcript	c.654G>A	p.Arg218=	synonymous_variant	6/9	1	NM_000673.7	P1
ADH7	ENST00000209665.8 linkuse as main transcript	c.690G>A	p.Arg230=	synonymous_variant	6/9	1			P40394-1
ADH7	ENST00000476959.5 linkuse as main transcript	c.714G>A	p.Arg238=	synonymous_variant	6/9	2			P40394-2
ADH7	ENST00000482593.5 linkuse as main transcript	c.483G>A	p.Arg161=	synonymous_variant	7/10	3

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20202

AN:

151930

Hom.:

1430

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.117

Gnomad OTH

AF:

0.139

GnomAD3 exomes

AF:

0.121

AC:

30480

AN:

251046

Hom.:

1986

AF XY:

0.120

AC XY:

16271

AN XY:

135652

show subpopulations

Gnomad AFR exome

AF:

0.167

Gnomad AMR exome

AF:

0.102

Gnomad ASJ exome

AF:

0.222

Gnomad EAS exome

AF:

0.102

Gnomad SAS exome

AF:

0.106

Gnomad FIN exome

AF:

0.144

Gnomad NFE exome

AF:

0.114

Gnomad OTH exome

AF:

0.129

GnomAD4 exome

AF:

0.115

AC:

168798

AN:

1461576

Hom.:

10296

Cov.:

AF XY:

0.115

AC XY:

83807

AN XY:

727090

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.103

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.119

Gnomad4 SAS exome

AF:

0.106

Gnomad4 FIN exome

AF:

0.144

Gnomad4 NFE exome

AF:

0.110

Gnomad4 OTH exome

AF:

0.126

GnomAD4 genome

AF:

0.133

AC:

20245

AN:

152048

Hom.:

1435

Cov.:

AF XY:

0.134

AC XY:

9945

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.160

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.202

Gnomad4 EAS

AF:

0.114

Gnomad4 SAS

AF:

0.102

Gnomad4 FIN

AF:

0.141

Gnomad4 NFE

AF:

0.117

Gnomad4 OTH

AF:

0.140

Alfa

AF:

0.123

Hom.:

2812

Bravo

AF:

0.134

Asia WGS

AF:

0.117

AC:

404

AN:

3478

EpiCase

AF:

0.117

EpiControl

AF:

0.110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

8.1

DANN

Benign

0.65

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