rs284786

Variant names:

• chr4-99412820-T-A
• rs284786
• NM_000673.7:c.*328A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-99412820-T-A
• chr4-99412820-T-C
• chr4-99412820-T-G

Variant summary

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

The NM_000673.7(ADH7):​c.*328A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 247,996 control chromosomes in the GnomAD database, including 17,137 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 0.36 (10968 hom., cov: 33)
  • Exomes 𝑓: 0.33 (6169 hom.)
• Consequence: ADH7 NM_000673.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000673.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADH7	NM_000673.7	MANE Select	c.*328A>T		3_prime_UTR	Exon 9 of 9	NP_000664.3	A0A0C4DG85
	ADH7	NM_001166504.2		c.*328A>T		3_prime_UTR	Exon 9 of 9	NP_001159976.1	P40394-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADH7	ENST00000437033.7	TSL:1 MANE Select	c.*328A>T		3_prime_UTR	Exon 9 of 9	ENSP00000414254.2	A0A0C4DG85
	ADH7	ENST00000209665.8	TSL:1	c.*328A>T		3_prime_UTR	Exon 9 of 9	ENSP00000209665.4	P40394-1
	ADH7	ENST00000476959.5	TSL:2	c.*328A>T		downstream_gene	N/A	ENSP00000420269.1	P40394-2

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55137 AN: 151942 Hom.: 10961 Cov.: 33

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.335

GnomAD4 exome AF: 0.331 AC: 31728 AN: 95936 Hom.: 6169 Cov.: 0 AF XY: 0.333 AC XY: 16615 AN XY: 49862

African (AFR) AF: 0.493 AC: 1398 AN: 2838

American (AMR) AF: 0.289 AC: 1148 AN: 3966

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 822 AN: 3324

East Asian (EAS) AF: 0.721 AC: 4710 AN: 6530

South Asian (SAS) AF: 0.433 AC: 2092 AN: 4830

European-Finnish (FIN) AF: 0.191 AC: 958 AN: 5014

Middle Eastern (MID) AF: 0.369 AC: 167 AN: 452

European-Non Finnish (NFE) AF: 0.295 AC: 18515 AN: 62800

Other (OTH) AF: 0.310 AC: 1918 AN: 6182

GnomAD4 genome AF: 0.363 AC: 55183 AN: 152060 Hom.: 10968 Cov.: 33 AF XY: 0.362 AC XY: 26917 AN XY: 74336

African (AFR) AF: 0.512 AC: 21244 AN: 41464

American (AMR) AF: 0.298 AC: 4547 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3470

East Asian (EAS) AF: 0.590 AC: 3057 AN: 5184

South Asian (SAS) AF: 0.454 AC: 2190 AN: 4822

European-Finnish (FIN) AF: 0.189 AC: 2003 AN: 10586

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20109 AN: 67942

Other (OTH) AF: 0.336 AC: 708 AN: 2106

Alfa AF: 0.187 Hom.: 370

Bravo AF: 0.378

Asia WGS AF: 0.424 AC: 1467 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.33
DANN	Benign	0.34
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs284786; hg19: chr4-100333977;