NM_001102470.2:c.120+1136T>C

Variant names:

• chr4-99215025-A-G
• rs9307238
• NM_001102470.2:c.120+1136T>C

Variant summary

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

The NM_001102470.2(ADH6):​c.120+1136T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,990 control chromosomes in the GnomAD database, including 24,959 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 0.57 (24959 hom., cov: 33)
• Consequence: ADH6 NM_001102470.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 6 publications found

Genes affected

ADH6 (HGNC:255): (alcohol dehydrogenase 6 (class V)) This gene encodes class V alcohol dehydrogenase, 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. This gene is expressed in the stomach as well as in the liver, and it contains a glucocorticoid response element upstream of its 5' UTR, which is a steroid hormone receptor binding site. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ENSG00000246090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADH6	NM_001102470.2	c.120+1136T>C		intron_variant	Intron 2 of 8	ENST00000394899.6	NP_001095940.1
ADH6	NM_000672.4	c.120+1136T>C		intron_variant	Intron 2 of 7		NP_000663.1
LOC100507053	NR_037884.1	n.3789+10594A>G		intron_variant	Intron 4 of 9
ADH6	NR_132990.2	n.214+1136T>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADH6	ENST00000394899.6	c.120+1136T>C		intron_variant	Intron 2 of 8	2	NM_001102470.2	ENSP00000378359.2

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85952 AN: 151874 Hom.: 24936 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.566 AC: 86022 AN: 151990 Hom.: 24959 Cov.: 33 AF XY: 0.565 AC XY: 41992 AN XY: 74276

African (AFR) AF: 0.644 AC: 26711 AN: 41454

American (AMR) AF: 0.601 AC: 9194 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1923 AN: 3468

East Asian (EAS) AF: 0.879 AC: 4552 AN: 5176

South Asian (SAS) AF: 0.562 AC: 2700 AN: 4808

European-Finnish (FIN) AF: 0.468 AC: 4938 AN: 10548

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34135 AN: 67938

Other (OTH) AF: 0.564 AC: 1190 AN: 2110

Alfa AF: 0.460 Hom.: 7464

Bravo AF: 0.581

Asia WGS AF: 0.630 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.42
DANN	Benign	0.68
PhyloP100		-2.1
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: rs9307238; hg19: chr4-100136182;