NM_001102470.2:c.1079T>G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001102470.2(ADH6):ā€‹c.1079T>Gā€‹(p.Val360Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,456,528 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/21 in silico tools predict 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 š‘“: 0.0000034 ( 0 hom. )

Consequence

ADH6
NM_001102470.2 missense

Scores

2
4
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.55
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ADH6NM_001102470.2 linkc.1079T>G p.Val360Gly missense_variant Exon 8 of 9 ENST00000394899.6 NP_001095940.1 P28332-2Q8IUN7
ADH6NM_000672.4 linkc.1079T>G p.Val360Gly missense_variant Exon 8 of 8 NP_000663.1 P28332-1Q8IUN7
ADH6NR_132990.2 linkn.814T>G non_coding_transcript_exon_variant Exon 6 of 7
LOC100507053NR_037884.1 linkn.3789+518A>C intron_variant Intron 4 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ADH6ENST00000394899.6 linkc.1079T>G p.Val360Gly missense_variant Exon 8 of 9 2 NM_001102470.2 ENSP00000378359.2 P28332-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000407
AC:
1
AN:
245894
Hom.:
0
AF XY:
0.00000752
AC XY:
1
AN XY:
132922
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000892
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000343
AC:
5
AN:
1456528
Hom.:
0
Cov.:
31
AF XY:
0.00000414
AC XY:
3
AN XY:
724410
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000450
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378
EpiCase
AF:
0.0000551
EpiControl
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.45
CADD
Benign
13
DANN
Benign
0.93
DEOGEN2
Benign
0.20
.;T
Eigen
Benign
-0.54
Eigen_PC
Benign
-0.61
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Uncertain
0.89
D;D
M_CAP
Benign
0.0049
T
MetaRNN
Uncertain
0.61
D;D
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.9
L;L
PrimateAI
Benign
0.37
T
PROVEAN
Uncertain
-2.4
N;N
REVEL
Benign
0.17
Sift
Pathogenic
0.0
D;D
Sift4G
Pathogenic
0.0
D;D
Polyphen
0.23
B;B
Vest4
0.35
MutPred
0.78
Gain of disorder (P = 0.0109);Gain of disorder (P = 0.0109);
MVP
0.21
MPC
0.18
ClinPred
0.57
D
GERP RS
0.93
Varity_R
0.065
gMVP
0.75

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs139932440; hg19: chr4-100126106; API