chr4-99216377-G-T

Variant names:

• chr4-99216377-G-T
• rs4699733
• NM_001102470.2:c.19-115C>A

Variant summary

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

The NM_001102470.2(ADH6):​c.19-115C>A variant causes a intron 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: 27)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ADH6 NM_001102470.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 7 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: 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=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001102470.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADH6	NM_001102470.2	MANE Select	c.19-115C>A		intron	N/A	NP_001095940.1
	ADH6	NM_000672.4		c.19-115C>A		intron	N/A	NP_000663.1
	LOC100507053	NR_037884.1		n.3789+11946G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADH6	ENST00000394899.6	TSL:2 MANE Select	c.19-115C>A		intron	N/A	ENSP00000378359.2
	ENSG00000246090	ENST00000500358.6	TSL:1	n.3789+11946G>T		intron	N/A
	ADH6	ENST00000237653.11	TSL:5	c.19-115C>A		intron	N/A	ENSP00000237653.7

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 320676 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 165362

African (AFR) AF: 0.00 AC: 0 AN: 8582

American (AMR) AF: 0.00 AC: 0 AN: 9024

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9832

East Asian (EAS) AF: 0.00 AC: 0 AN: 23838

South Asian (SAS) AF: 0.00 AC: 0 AN: 8406

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28228

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1530

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 213052

Other (OTH) AF: 0.00 AC: 0 AN: 18184

GnomAD4 genome Cov.: 27

Alfa AF: 0.00 Hom.: 1581

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.14
PhyloP100		-0.73

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: rs4699733; hg19: chr4-100137534;