rs9990
Variant names:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_032804.6(ADO):c.*2306C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 167,054 control chromosomes in the GnomAD database, including 5,438 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 0.23 ( 5032 hom., cov: 33)
Exomes 𝑓: 0.22 ( 406 hom. )
Consequence
ADO
NM_032804.6 3_prime_UTR
NM_032804.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0200
Publications
11 publications found
Genes affected
ADO (HGNC:23506): (2-aminoethanethiol dioxygenase) Human thiol dioxygenases include cysteine dioxygenase (CDO; MIM 603943) and cysteamine (2-aminoethanethiol) dioxygenase (ADO; EC 1.13.11.19). CDO adds 2 oxygen atoms to free cysteine, whereas ADO adds 2 oxygen atoms to free cysteamine to form hypotaurine (Dominy et al., 2007 [PubMed 17581819]).[supplied by OMIM, Mar 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.24).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.230 AC: 34914AN: 151924Hom.: 5009 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
34914
AN:
151924
Hom.:
Cov.:
33
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: 0.223 AC: 3346AN: 15012Hom.: 406 Cov.: 0 AF XY: 0.227 AC XY: 1623AN XY: 7140 show subpopulations
GnomAD4 exome
AF:
AC:
3346
AN:
15012
Hom.:
Cov.:
0
AF XY:
AC XY:
1623
AN XY:
7140
show subpopulations
African (AFR)
AF:
AC:
2
AN:
4
American (AMR)
AF:
AC:
2
AN:
4
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
AC:
18
AN:
138
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
3291
AN:
14690
Middle Eastern (MID)
AF:
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
AC:
11
AN:
84
Other (OTH)
AF:
AC:
22
AN:
90
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
142
284
425
567
709
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<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: 0.230 AC: 35002AN: 152042Hom.: 5032 Cov.: 33 AF XY: 0.234 AC XY: 17418AN XY: 74320 show subpopulations
GnomAD4 genome
AF:
AC:
35002
AN:
152042
Hom.:
Cov.:
33
AF XY:
AC XY:
17418
AN XY:
74320
show subpopulations
African (AFR)
AF:
AC:
14988
AN:
41452
American (AMR)
AF:
AC:
4753
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
249
AN:
3468
East Asian (EAS)
AF:
AC:
2249
AN:
5174
South Asian (SAS)
AF:
AC:
1161
AN:
4822
European-Finnish (FIN)
AF:
AC:
2249
AN:
10554
Middle Eastern (MID)
AF:
AC:
50
AN:
294
European-Non Finnish (NFE)
AF:
AC:
8685
AN:
67984
Other (OTH)
AF:
AC:
448
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1288
2576
3864
5152
6440
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
354
708
1062
1416
1770
<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:
1248
AN:
3474
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.