4-99202619-C-T

Variant names:

• chr4-99202619-C-T
• rs2000864
• ENST00000500358.6:n.3715-1738C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000881182.1(ADH6):​c.*1600G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ADH6 ENST00000881182.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 7 publications found

Genes affected

ENSG00000246090 (HGNC:):

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000881182.1. 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
	LOC100507053	NR_037884.1		n.3715-1738C>T		intron	N/A
	ADH6	NM_001102470.2	MANE Select	c.*1600G>A		downstream_gene	N/A	NP_001095940.1	P28332-2
	ADH6	NM_000672.4		c.*2302G>A		downstream_gene	N/A	NP_000663.1	P28332-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000246090	ENST00000500358.6	TSL:1	n.3715-1738C>T		intron	N/A
	ADH6	ENST00000881182.1		c.*1600G>A		3_prime_UTR	Exon 8 of 8	ENSP00000551241.1
	ENSG00000246090	ENST00000506160.1	TSL:4	n.333-1738C>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 244418 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 123926

African (AFR) AF: 0.00 AC: 0 AN: 7112

American (AMR) AF: 0.00 AC: 0 AN: 7402

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9156

East Asian (EAS) AF: 0.00 AC: 0 AN: 22872

South Asian (SAS) AF: 0.00 AC: 0 AN: 2806

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20746

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1276

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 156770

Other (OTH) AF: 0.00 AC: 0 AN: 16278

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.86
DANN	Benign	0.96
PhyloP100		-0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2000864; hg19: chr4-100123776;