4-99412110-G-A

Variant names:

• chr4-99412110-G-A
• rs729147
• NM_000673.7:c.*1038C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000673.7(ADH7):​c.*1038C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 151,924 control chromosomes in the GnomAD database, including 46,135 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 0.78 (46135 hom., cov: 31)
• Consequence: ADH7 NM_000673.7 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 14 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADH7	NM_000673.7	c.*1038C>T		downstream_gene_variant		ENST00000437033.7	NP_000664.3
ADH7	NM_001166504.2	c.*1038C>T		downstream_gene_variant			NP_001159976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADH7	ENST00000437033.7	c.*1038C>T		downstream_gene_variant		1	NM_000673.7	ENSP00000414254.2
ADH7	ENST00000209665.8	c.*1038C>T		downstream_gene_variant		1		ENSP00000209665.4

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117703 AN: 151806 Hom.: 46101 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.731

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.775 AC: 117789 AN: 151924 Hom.: 46135 Cov.: 31 AF XY: 0.769 AC XY: 57115 AN XY: 74244

African (AFR) AF: 0.840 AC: 34819 AN: 41464

American (AMR) AF: 0.610 AC: 9312 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2349 AN: 3464

East Asian (EAS) AF: 0.650 AC: 3358 AN: 5170

South Asian (SAS) AF: 0.705 AC: 3389 AN: 4808

European-Finnish (FIN) AF: 0.770 AC: 8111 AN: 10538

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 53997 AN: 67896

Other (OTH) AF: 0.728 AC: 1538 AN: 2114

Alfa AF: 0.780 Hom.: 212172

Bravo AF: 0.764

Asia WGS AF: 0.600 AC: 2086 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.22
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs729147; hg19: chr4-100333267;