rs11259936

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_207517.3(ADAMTSL3):​c.1701-1262A>C 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 152,042 control chromosomes in the GnomAD database, including 30,998 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 ( 30998 hom., cov: 32)

Consequence

ADAMTSL3
NM_207517.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.789

Publications

47 publications found
Variant links:
Genes affected
ADAMTSL3 (HGNC:14633): (ADAMTS like 3) Predicted to be involved in extracellular matrix organization. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ADAMTSL3NM_207517.3 linkc.1701-1262A>C intron_variant Intron 15 of 29 ENST00000286744.10 NP_997400.2 P82987-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ADAMTSL3ENST00000286744.10 linkc.1701-1262A>C intron_variant Intron 15 of 29 1 NM_207517.3 ENSP00000286744.5 P82987-1
ADAMTSL3ENST00000567476.1 linkc.1701-1262A>C intron_variant Intron 15 of 29 1 ENSP00000456313.1 P82987-2
ADAMTSL3ENST00000561483.5 linkn.1916-1262A>C intron_variant Intron 15 of 26 5

Frequencies

GnomAD3 genomes
AF:
0.627
AC:
95252
AN:
151924
Hom.:
30950
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.787
Gnomad AMI
AF:
0.575
Gnomad AMR
AF:
0.707
Gnomad ASJ
AF:
0.616
Gnomad EAS
AF:
0.744
Gnomad SAS
AF:
0.614
Gnomad FIN
AF:
0.513
Gnomad MID
AF:
0.668
Gnomad NFE
AF:
0.523
Gnomad OTH
AF:
0.617
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.627
AC:
95362
AN:
152042
Hom.:
30998
Cov.:
32
AF XY:
0.628
AC XY:
46716
AN XY:
74340
show subpopulations
African (AFR)
AF:
0.787
AC:
32651
AN:
41490
American (AMR)
AF:
0.708
AC:
10822
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.616
AC:
2136
AN:
3466
East Asian (EAS)
AF:
0.744
AC:
3845
AN:
5166
South Asian (SAS)
AF:
0.613
AC:
2950
AN:
4814
European-Finnish (FIN)
AF:
0.513
AC:
5413
AN:
10550
Middle Eastern (MID)
AF:
0.673
AC:
198
AN:
294
European-Non Finnish (NFE)
AF:
0.523
AC:
35521
AN:
67950
Other (OTH)
AF:
0.616
AC:
1303
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1737
3474
5211
6948
8685
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
766
1532
2298
3064
3830
<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:
0.560
Hom.:
76255
Bravo
AF:
0.650
Asia WGS
AF:
0.674
AC:
2343
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.13
DANN
Benign
0.57
PhyloP100
-0.79
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs11259936; hg19: chr15-84580582; API