GeneBe

rs1154400

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000500358.6(ENSG00000246090):​n.3C>A variant causes a non coding transcript exon 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

ENSG00000246090
ENST00000500358.6 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.318

Publications

22 publications found
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]
ADH5 Gene-Disease associations (from GenCC):
  • AMED syndrome, digenic
    Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

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=-0.75).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500358.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
LOC100507053
NR_037884.1
n.3C>A
non_coding_transcript_exon
Exon 1 of 10
ADH5
NM_000671.4
MANE Select
c.-159G>T
upstream_gene
N/ANP_000662.3

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ENSG00000246090
ENST00000500358.6
TSL:1
n.3C>A
non_coding_transcript_exon
Exon 1 of 10
ENSG00000246090
ENST00000670724.2
n.55C>A
non_coding_transcript_exon
Exon 1 of 3
ENSG00000246090
ENST00000671105.1
n.27C>A
non_coding_transcript_exon
Exon 1 of 2

Frequencies

GnomAD3 genomes
Cov.:
27
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
298912
Hom.:
0
Cov.:
4
AF XY:
0.00
AC XY:
0
AN XY:
157952
African (AFR)
AF:
0.00
AC:
0
AN:
8696
American (AMR)
AF:
0.00
AC:
0
AN:
12624
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
9772
East Asian (EAS)
AF:
0.00
AC:
0
AN:
21596
South Asian (SAS)
AF:
0.00
AC:
0
AN:
21590
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
24022
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1298
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
181540
Other (OTH)
AF:
0.00
AC:
0
AN:
17774
GnomAD4 genome
Cov.:
27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
0.34
DANN
Benign
0.52
PhyloP100
-0.32
PromoterAI
-0.13
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs1154400; hg19: chr4-100010010; API