rs1944766

Variant summary

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

The ENST00000680146.1(ADAMTSL1):​c.207+51301C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 151,910 control chromosomes in the GnomAD database, including 27,631 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 0.60 ( 27631 hom., cov: 33)

Consequence

ADAMTSL1
ENST00000680146.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.272

Publications

10 publications found
Variant links:
Genes affected
ADAMTSL1 (HGNC:14632): (ADAMTS like 1) This gene encodes a secreted protein and member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motif) family. This protein lacks the metalloproteinase and disintegrin-like domains, which are typical of the ADAMTS family, but contains other ADAMTS domains, including the thrombospondin type 1 motif. This protein may have important functions in the extracellular matrix. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2008]

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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ADAMTSL1XM_011518063.3 linkc.261+51301C>A intron_variant Intron 3 of 30 XP_011516365.1
ADAMTSL1XM_017015310.2 linkc.219+51301C>A intron_variant Intron 2 of 29 XP_016870799.1
ADAMTSL1XM_011518064.4 linkc.216+51301C>A intron_variant Intron 2 of 29 XP_011516366.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ADAMTSL1ENST00000680146.1 linkc.207+51301C>A intron_variant Intron 2 of 29 ENSP00000505591.1 A0A7P0T9B9

Frequencies

GnomAD3 genomes
AF:
0.602
AC:
91396
AN:
151792
Hom.:
27596
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.649
Gnomad AMI
AF:
0.493
Gnomad AMR
AF:
0.638
Gnomad ASJ
AF:
0.595
Gnomad EAS
AF:
0.464
Gnomad SAS
AF:
0.521
Gnomad FIN
AF:
0.587
Gnomad MID
AF:
0.666
Gnomad NFE
AF:
0.586
Gnomad OTH
AF:
0.611
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.602
AC:
91482
AN:
151910
Hom.:
27631
Cov.:
33
AF XY:
0.600
AC XY:
44548
AN XY:
74238
show subpopulations
African (AFR)
AF:
0.649
AC:
26896
AN:
41428
American (AMR)
AF:
0.638
AC:
9742
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.595
AC:
2065
AN:
3470
East Asian (EAS)
AF:
0.463
AC:
2395
AN:
5168
South Asian (SAS)
AF:
0.518
AC:
2494
AN:
4812
European-Finnish (FIN)
AF:
0.587
AC:
6179
AN:
10534
Middle Eastern (MID)
AF:
0.658
AC:
192
AN:
292
European-Non Finnish (NFE)
AF:
0.586
AC:
39773
AN:
67926
Other (OTH)
AF:
0.614
AC:
1297
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1909
3819
5728
7638
9547
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:
0.589
Hom.:
49875
Bravo
AF:
0.608
Asia WGS
AF:
0.517
AC:
1785
AN:
3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.9
DANN
Benign
0.32
PhyloP100
0.27

Splicing

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

Publications

Other links and lift over

dbSNP: rs1944766; hg19: chr9-18215280; API