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rs1154415

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000671.4(ADH5):c.345-959A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,082 control chromosomes in the GnomAD database, including 10,342 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 0.34 ( 10342 hom., cov: 32)

Consequence

ADH5
NM_000671.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.345
Variant links:
Genes affected
ADH5 (HGNC:253): (alcohol dehydrogenase 5 (class III), chi polypeptide) This gene encodes 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 encoded protein forms a homodimer. It has virtually no activity for ethanol oxidation, but exhibits high activity for oxidation of long-chain primary alcohols and for oxidation of S-hydroxymethyl-glutathione, a spontaneous adduct between formaldehyde and glutathione. This enzyme is an important component of cellular metabolism for the elimination of formaldehyde, a potent irritant and sensitizing agent that causes lacrymation, rhinitis, pharyngitis, and contact dermatitis. The human genome contains several non-transcribed pseudogenes related to this gene. [provided by RefSeq, Oct 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADH5NM_000671.4 linkuse as main transcriptc.345-959A>G intron_variant ENST00000296412.14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADH5ENST00000296412.14 linkuse as main transcriptc.345-959A>G intron_variant 1 NM_000671.4 P1

Frequencies

GnomAD3 genomes
AF:
0.339
AC:
51510
AN:
151964
Hom.:
10337
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.136
Gnomad AMI
AF:
0.392
Gnomad AMR
AF:
0.328
Gnomad ASJ
AF:
0.391
Gnomad EAS
AF:
0.135
Gnomad SAS
AF:
0.520
Gnomad FIN
AF:
0.449
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.446
Gnomad OTH
AF:
0.351
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.339
AC:
51515
AN:
152082
Hom.:
10342
Cov.:
32
AF XY:
0.342
AC XY:
25426
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.135
Gnomad4 AMR
AF:
0.328
Gnomad4 ASJ
AF:
0.391
Gnomad4 EAS
AF:
0.135
Gnomad4 SAS
AF:
0.521
Gnomad4 FIN
AF:
0.449
Gnomad4 NFE
AF:
0.446
Gnomad4 OTH
AF:
0.355
Alfa
AF:
0.413
Hom.:
13078
Bravo
AF:
0.314
Asia WGS
AF:
0.378
AC:
1317
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
2.4
Dann
Benign
0.59

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: rs1154415; hg19: chr4-99999033; API