rs1827567

Variant names:

• chr4-99414945-G-A
• rs1827567
• NM_000673.7:c.1100+533C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-99414945-G-A
• chr4-99414945-G-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.1100+533C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,158 control chromosomes in the GnomAD database, including 3,835 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 0.21 (3835 hom., cov: 32)
• Consequence: ADH7 NM_000673.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADH7	NM_000673.7	c.1100+533C>T		intron_variant	Intron 8 of 8	ENST00000437033.7	NP_000664.3
ADH7	NM_001166504.2	c.1160+533C>T		intron_variant	Intron 8 of 8		NP_001159976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADH7	ENST00000437033.7	c.1100+533C>T		intron_variant	Intron 8 of 8	1	NM_000673.7	ENSP00000414254.2

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32311 AN: 152040 Hom.: 3833 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.212 AC: 32324 AN: 152158 Hom.: 3835 Cov.: 32 AF XY: 0.213 AC XY: 15818 AN XY: 74374

African (AFR) AF: 0.153 AC: 6336 AN: 41506

American (AMR) AF: 0.204 AC: 3121 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3464

East Asian (EAS) AF: 0.512 AC: 2645 AN: 5166

South Asian (SAS) AF: 0.355 AC: 1714 AN: 4824

European-Finnish (FIN) AF: 0.133 AC: 1410 AN: 10594

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.229 AC: 15605 AN: 68012

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.232 Hom.: 6452

Bravo AF: 0.216

Asia WGS AF: 0.296 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.23
PhyloP100		-0.17
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: rs1827567; hg19: chr4-100336102;