rs11259933
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_207517.3(ADAMTSL3):c.1701-1688G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,108 control chromosomes in the GnomAD database, including 31,024 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 ( 31024 hom., cov: 33)
Consequence
ADAMTSL3
NM_207517.3 intron
NM_207517.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.191
Publications
25 publications found
Genes affected
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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAMTSL3 | ENST00000286744.10 | c.1701-1688G>A | intron_variant | Intron 15 of 29 | 1 | NM_207517.3 | ENSP00000286744.5 | |||
ADAMTSL3 | ENST00000567476.1 | c.1701-1688G>A | intron_variant | Intron 15 of 29 | 1 | ENSP00000456313.1 | ||||
ADAMTSL3 | ENST00000561483.5 | n.1916-1688G>A | intron_variant | Intron 15 of 26 | 5 |
Frequencies
GnomAD3 genomes AF: 0.627 AC: 95311AN: 151990Hom.: 30976 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
95311
AN:
151990
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.627 AC: 95421AN: 152108Hom.: 31024 Cov.: 33 AF XY: 0.629 AC XY: 46746AN XY: 74364 show subpopulations
GnomAD4 genome
AF:
AC:
95421
AN:
152108
Hom.:
Cov.:
33
AF XY:
AC XY:
46746
AN XY:
74364
show subpopulations
African (AFR)
AF:
AC:
32680
AN:
41518
American (AMR)
AF:
AC:
10823
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
2142
AN:
3468
East Asian (EAS)
AF:
AC:
3853
AN:
5172
South Asian (SAS)
AF:
AC:
2961
AN:
4828
European-Finnish (FIN)
AF:
AC:
5414
AN:
10564
Middle Eastern (MID)
AF:
AC:
198
AN:
294
European-Non Finnish (NFE)
AF:
AC:
35525
AN:
67956
Other (OTH)
AF:
AC:
1302
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1742
3484
5227
6969
8711
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2343
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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