rs17588403

Variant names:

• chr4-99413292-T-A
• rs17588403
• NM_000673.7:c.1101-120A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-99413292-T-A
• chr4-99413292-T-C

Variant summary

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

The NM_000673.7(ADH7):​c.1101-120A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 1,096,422 control chromosomes in the GnomAD database, including 16,712 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 0.15 (1925 hom., cov: 32)
  • Exomes 𝑓: 0.17 (14787 hom.)
• Consequence: ADH7 NM_000673.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744
• Publications: 6 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 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.1101-120A>T		intron	N/A	NP_000664.3	A0A0C4DG85
	ADH7	NM_001166504.2		c.1161-120A>T		intron	N/A	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.1101-120A>T		intron	N/A	ENSP00000414254.2	A0A0C4DG85
	ADH7	ENST00000209665.8	TSL:1	c.1137-120A>T		intron	N/A	ENSP00000209665.4	P40394-1
	ADH7	ENST00000476959.5	TSL:2	c.1161-120A>T		intron	N/A	ENSP00000420269.1	P40394-2

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23163 AN: 152116 Hom.: 1918 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0710

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.168 AC: 158663 AN: 944188 Hom.: 14787 AF XY: 0.165 AC XY: 80235 AN XY: 485824

African (AFR) AF: 0.110 AC: 2378 AN: 21552

American (AMR) AF: 0.0930 AC: 3182 AN: 34208

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 2597 AN: 19814

East Asian (EAS) AF: 0.0224 AC: 788 AN: 35178

South Asian (SAS) AF: 0.0665 AC: 4378 AN: 65824

European-Finnish (FIN) AF: 0.185 AC: 7960 AN: 43100

Middle Eastern (MID) AF: 0.101 AC: 462 AN: 4556

European-Non Finnish (NFE) AF: 0.193 AC: 130592 AN: 677482

Other (OTH) AF: 0.149 AC: 6326 AN: 42474

GnomAD4 genome AF: 0.152 AC: 23193 AN: 152234 Hom.: 1925 Cov.: 32 AF XY: 0.148 AC XY: 11033 AN XY: 74434

African (AFR) AF: 0.118 AC: 4907 AN: 41546

American (AMR) AF: 0.118 AC: 1809 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3472

East Asian (EAS) AF: 0.0176 AC: 91 AN: 5184

South Asian (SAS) AF: 0.0725 AC: 350 AN: 4826

European-Finnish (FIN) AF: 0.182 AC: 1927 AN: 10596

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13175 AN: 68008

Other (OTH) AF: 0.128 AC: 270 AN: 2112

Alfa AF: 0.179 Hom.: 338

Bravo AF: 0.147

Asia WGS AF: 0.0510 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.79
PhyloP100		-0.74
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: rs17588403; hg19: chr4-100334449;