rs284786

chr4-99412820-T-Achr4-99412820-T-Cchr4-99412820-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADH7	NM_000673.7	c.*328A>T		3_prime_UTR_variant	9/9	ENST00000437033.7
ADH7	NM_001166504.2	c.*328A>T		3_prime_UTR_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADH7	ENST00000437033.7	c.*328A>T		3_prime_UTR_variant	9/9	1	NM_000673.7	P1
ADH7	ENST00000209665.8	c.*328A>T		3_prime_UTR_variant	9/9	1

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

Gnomad4 AFR exome AF: 0.493

Gnomad4 AMR exome AF: 0.289

Gnomad4 ASJ exome AF: 0.247

Gnomad4 EAS exome AF: 0.721

Gnomad4 SAS exome AF: 0.433

Gnomad4 FIN exome AF: 0.191

Gnomad4 NFE exome AF: 0.295

Gnomad4 OTH exome AF: 0.310

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

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.336

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.33
Dann	Benign	0.34

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

Other links and lift over

dbSNP: rs284786; hg19: chr4-100333977;