rs402007
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006988.5(ADAMTS1):c.-47G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 1,477,456 control chromosomes in the GnomAD database, including 427,087 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 0.77 ( 46310 hom., cov: 34)
Exomes 𝑓: 0.75 ( 380777 hom. )
Consequence
ADAMTS1
NM_006988.5 5_prime_UTR
NM_006988.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.123
Publications
18 publications found
Genes affected
ADAMTS1 (HGNC:217): (ADAM metallopeptidase with thrombospondin type 1 motif 1) This gene encodes a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motif) protein family. Members of the family share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. Individual members of this family differ in the number of C-terminal TS motifs, and some have unique C-terminal domains. The protein encoded by this gene contains two disintegrin loops and three C-terminal TS motifs and has anti-angiogenic activity. The expression of this gene may be associated with various inflammatory processes as well as development of cancer cachexia. This gene is likely to be necessary for normal growth, fertility, and organ morphology and function. [provided by RefSeq, Jul 2008]
ADAMTS1 Gene-Disease associations (from GenCC):
- autosomal dominant prognathismInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
Genome browser will be placed here
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=-0.7).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.772 AC: 117320AN: 152056Hom.: 46256 Cov.: 34 show subpopulations
GnomAD3 genomes
AF:
AC:
117320
AN:
152056
Hom.:
Cov.:
34
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:
GnomAD2 exomes AF: 0.691 AC: 96054AN: 138992 AF XY: 0.699 show subpopulations
GnomAD2 exomes
AF:
AC:
96054
AN:
138992
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.754 AC: 999600AN: 1325284Hom.: 380777 Cov.: 47 AF XY: 0.752 AC XY: 485707AN XY: 645634 show subpopulations
GnomAD4 exome
AF:
AC:
999600
AN:
1325284
Hom.:
Cov.:
47
AF XY:
AC XY:
485707
AN XY:
645634
show subpopulations
African (AFR)
AF:
AC:
25810
AN:
28676
American (AMR)
AF:
AC:
13372
AN:
27650
Ashkenazi Jewish (ASJ)
AF:
AC:
14346
AN:
19104
East Asian (EAS)
AF:
AC:
16588
AN:
37580
South Asian (SAS)
AF:
AC:
45517
AN:
64778
European-Finnish (FIN)
AF:
AC:
28877
AN:
36722
Middle Eastern (MID)
AF:
AC:
3329
AN:
5196
European-Non Finnish (NFE)
AF:
AC:
810927
AN:
1050680
Other (OTH)
AF:
AC:
40834
AN:
54898
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.477
Heterozygous variant carriers
0
12159
24318
36478
48637
60796
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
20186
40372
60558
80744
100930
<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: 0.772 AC: 117426AN: 152172Hom.: 46310 Cov.: 34 AF XY: 0.766 AC XY: 57002AN XY: 74390 show subpopulations
GnomAD4 genome
AF:
AC:
117426
AN:
152172
Hom.:
Cov.:
34
AF XY:
AC XY:
57002
AN XY:
74390
show subpopulations
African (AFR)
AF:
AC:
37061
AN:
41556
American (AMR)
AF:
AC:
9056
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
2638
AN:
3472
East Asian (EAS)
AF:
AC:
2215
AN:
5136
South Asian (SAS)
AF:
AC:
3340
AN:
4818
European-Finnish (FIN)
AF:
AC:
8473
AN:
10608
Middle Eastern (MID)
AF:
AC:
189
AN:
292
European-Non Finnish (NFE)
AF:
AC:
52312
AN:
67978
Other (OTH)
AF:
AC:
1523
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1347
2694
4040
5387
6734
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
852
1704
2556
3408
4260
<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:
2195
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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