chr4-99210006-G-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001102470.2(ADH6):c.567+76C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 1,440,230 control chromosomes in the GnomAD database, including 231,794 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 0.63 ( 32083 hom., cov: 32)
Exomes 𝑓: 0.55 ( 199711 hom. )
Consequence
ADH6
NM_001102470.2 intron
NM_001102470.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.28
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]
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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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADH6 | NM_001102470.2 | c.567+76C>G | intron_variant | Intron 5 of 8 | ENST00000394899.6 | NP_001095940.1 | ||
ADH6 | NM_000672.4 | c.567+76C>G | intron_variant | Intron 5 of 7 | NP_000663.1 | |||
LOC100507053 | NR_037884.1 | n.3789+5575G>C | intron_variant | Intron 4 of 9 | ||||
ADH6 | NR_132990.2 | n.302+409C>G | intron_variant | Intron 3 of 6 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.634 AC: 96273AN: 151892Hom.: 32031 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
96273
AN:
151892
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: 0.549 AC: 707872AN: 1288220Hom.: 199711 AF XY: 0.549 AC XY: 355471AN XY: 647340 show subpopulations
GnomAD4 exome
AF:
AC:
707872
AN:
1288220
Hom.:
AF XY:
AC XY:
355471
AN XY:
647340
show subpopulations
African (AFR)
AF:
AC:
25206
AN:
29966
American (AMR)
AF:
AC:
26065
AN:
42940
Ashkenazi Jewish (ASJ)
AF:
AC:
14275
AN:
24616
East Asian (EAS)
AF:
AC:
34487
AN:
38692
South Asian (SAS)
AF:
AC:
44962
AN:
81386
European-Finnish (FIN)
AF:
AC:
21720
AN:
43440
Middle Eastern (MID)
AF:
AC:
2972
AN:
5450
European-Non Finnish (NFE)
AF:
AC:
507542
AN:
967086
Other (OTH)
AF:
AC:
30643
AN:
54644
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
15580
31159
46739
62318
77898
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.634 AC: 96380AN: 152010Hom.: 32083 Cov.: 32 AF XY: 0.632 AC XY: 46985AN XY: 74294 show subpopulations
GnomAD4 genome
AF:
AC:
96380
AN:
152010
Hom.:
Cov.:
32
AF XY:
AC XY:
46985
AN XY:
74294
show subpopulations
African (AFR)
AF:
AC:
34369
AN:
41468
American (AMR)
AF:
AC:
9595
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
AC:
2020
AN:
3466
East Asian (EAS)
AF:
AC:
4540
AN:
5166
South Asian (SAS)
AF:
AC:
2756
AN:
4820
European-Finnish (FIN)
AF:
AC:
5280
AN:
10568
Middle Eastern (MID)
AF:
AC:
158
AN:
294
European-Non Finnish (NFE)
AF:
AC:
35826
AN:
67950
Other (OTH)
AF:
AC:
1303
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1688
3376
5064
6752
8440
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2247
AN:
3478
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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