chr4-99428309-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000673.7(ADH7):c.260-135A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0164 in 1,219,384 control chromosomes in the GnomAD database, including 4,000 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 0.015 ( 419 hom., cov: 32)
Exomes 𝑓: 0.017 ( 3581 hom. )
Consequence
ADH7
NM_000673.7 intron
NM_000673.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.742
Publications
4 publications found
Genes affected
ADH7 (HGNC:256): (alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide) This gene encodes class IV alcohol dehydrogenase 7 mu or sigma subunit, 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. The enzyme encoded by this gene is inefficient in ethanol oxidation, but is the most active as a retinol dehydrogenase; thus it may participate in the synthesis of retinoic acid, a hormone important for cellular differentiation. The expression of this gene is much more abundant in stomach than liver, thus differing from the other known gene family members. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADH7 | ENST00000437033.7 | c.260-135A>G | intron_variant | Intron 3 of 8 | 1 | NM_000673.7 | ENSP00000414254.2 |
Frequencies
GnomAD3 genomes AF: 0.0150 AC: 2289AN: 152192Hom.: 420 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2289
AN:
152192
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0167 AC: 17770AN: 1067074Hom.: 3581 AF XY: 0.0162 AC XY: 8712AN XY: 536384 show subpopulations
GnomAD4 exome
AF:
AC:
17770
AN:
1067074
Hom.:
AF XY:
AC XY:
8712
AN XY:
536384
show subpopulations
African (AFR)
AF:
AC:
11
AN:
23944
American (AMR)
AF:
AC:
35
AN:
28532
Ashkenazi Jewish (ASJ)
AF:
AC:
106
AN:
19614
East Asian (EAS)
AF:
AC:
15700
AN:
35538
South Asian (SAS)
AF:
AC:
189
AN:
63588
European-Finnish (FIN)
AF:
AC:
5
AN:
44598
Middle Eastern (MID)
AF:
AC:
8
AN:
4546
European-Non Finnish (NFE)
AF:
AC:
1135
AN:
800162
Other (OTH)
AF:
AC:
581
AN:
46552
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
581
1162
1744
2325
2906
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
184
368
552
736
920
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.0150 AC: 2284AN: 152310Hom.: 419 Cov.: 32 AF XY: 0.0175 AC XY: 1304AN XY: 74482 show subpopulations
GnomAD4 genome
AF:
AC:
2284
AN:
152310
Hom.:
Cov.:
32
AF XY:
AC XY:
1304
AN XY:
74482
show subpopulations
African (AFR)
AF:
AC:
18
AN:
41596
American (AMR)
AF:
AC:
33
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
26
AN:
3470
East Asian (EAS)
AF:
AC:
2048
AN:
5170
South Asian (SAS)
AF:
AC:
25
AN:
4828
European-Finnish (FIN)
AF:
AC:
1
AN:
10630
Middle Eastern (MID)
AF:
AC:
2
AN:
294
European-Non Finnish (NFE)
AF:
AC:
118
AN:
68014
Other (OTH)
AF:
AC:
13
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
68
135
203
270
338
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
40
80
120
160
200
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
340
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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