Variant chr4-99435309-A-G 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.-76T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,597,230 control chromosomes in the GnomAD database, including 13,866 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 0.10 ( 1063 hom., cov: 32)

Exomes 𝑓: 0.13 ( 12803 hom. )

Consequence

ADH7
NM_000673.7 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.498

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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 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.-76T>C		5_prime_UTR_variant	1/9	ENST00000437033.7	NP_000664.3	P40394

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ADH7	ENST00000437033.7 linkuse as main transcript	c.-76T>C	5_prime_UTR_variant	1/9	1	NM_000673.7	ENSP00000414254.2	A0A0C4DG85
ADH7	ENST00000209665.8 linkuse as main transcript	c.-40T>C	5_prime_UTR_variant	1/9	1		ENSP00000209665.4	P40394-1
ADH7	ENST00000482593.5 linkuse as main transcript	c.-360T>C	upstream_gene_variant		3		ENSP00000420613.1	E9PFG0

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15956

AN:

152092

Hom.:

1064

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0388

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.0867

Gnomad ASJ

AF:

0.128

Gnomad EAS

AF:

0.0827

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.136

Gnomad OTH

AF:

0.101

GnomAD3 exomes

AF:

0.124

AC:

29384

AN:

236710

Hom.:

2070

AF XY:

0.131

AC XY:

16748

AN XY:

127592

show subpopulations

Gnomad AFR exome

AF:

0.0377

Gnomad AMR exome

AF:

0.0747

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.0875

Gnomad SAS exome

AF:

0.159

Gnomad FIN exome

AF:

0.167

Gnomad NFE exome

AF:

0.141

Gnomad OTH exome

AF:

0.129

GnomAD4 exome

AF:

0.129

AC:

186685

AN:

1445020

Hom.:

12803

Cov.:

AF XY:

0.131

AC XY:

94420

AN XY:

718722

show subpopulations

Gnomad4 AFR exome

AF:

0.0387

Gnomad4 AMR exome

AF:

0.0739

Gnomad4 ASJ exome

AF:

0.125

Gnomad4 EAS exome

AF:

0.0473

Gnomad4 SAS exome

AF:

0.162

Gnomad4 FIN exome

AF:

0.173

Gnomad4 NFE exome

AF:

0.133

Gnomad4 OTH exome

AF:

0.125

GnomAD4 genome

AF:

0.105

AC:

15947

AN:

152210

Hom.:

1063

Cov.:

AF XY:

0.107

AC XY:

7943

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0388

Gnomad4 AMR

AF:

0.0865

Gnomad4 ASJ

AF:

0.128

Gnomad4 EAS

AF:

0.0829

Gnomad4 SAS

AF:

0.150

Gnomad4 FIN

AF:

0.173

Gnomad4 NFE

AF:

0.136

Gnomad4 OTH

AF:

0.0997

Alfa

AF:

0.125

Hom.:

2662

Bravo

AF:

0.0916

Asia WGS

AF:

0.106

AC:

368

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.7

DANN

Benign

0.74

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