9-17979580-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000680146.1(ADAMTSL1):​c.87+72658T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,206 control chromosomes in the GnomAD database, including 23,072 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 0.53 ( 23072 hom., cov: 29)

Consequence

ADAMTSL1
ENST00000680146.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.502
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ADAMTSL1XM_011518063.3 linkc.141+46555T>C intron_variant Intron 2 of 30 XP_011516365.1
ADAMTSL1XM_011518064.4 linkc.96+72658T>C intron_variant Intron 1 of 29 XP_011516366.1
ADAMTSL1XM_017015311.2 linkc.141+46555T>C intron_variant Intron 2 of 29 XP_016870800.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ADAMTSL1ENST00000680146.1 linkc.87+72658T>C intron_variant Intron 1 of 29 ENSP00000505591.1 A0A7P0T9B9

Frequencies

GnomAD3 genomes
AF:
0.531
AC:
80211
AN:
151086
Hom.:
23062
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.308
Gnomad AMI
AF:
0.602
Gnomad AMR
AF:
0.622
Gnomad ASJ
AF:
0.505
Gnomad EAS
AF:
0.920
Gnomad SAS
AF:
0.605
Gnomad FIN
AF:
0.585
Gnomad MID
AF:
0.419
Gnomad NFE
AF:
0.604
Gnomad OTH
AF:
0.524
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.531
AC:
80252
AN:
151206
Hom.:
23072
Cov.:
29
AF XY:
0.536
AC XY:
39563
AN XY:
73838
show subpopulations
Gnomad4 AFR
AF:
0.308
Gnomad4 AMR
AF:
0.622
Gnomad4 ASJ
AF:
0.505
Gnomad4 EAS
AF:
0.921
Gnomad4 SAS
AF:
0.604
Gnomad4 FIN
AF:
0.585
Gnomad4 NFE
AF:
0.604
Gnomad4 OTH
AF:
0.528
Alfa
AF:
0.573
Hom.:
10152
Bravo
AF:
0.529
Asia WGS
AF:
0.703
AC:
2443
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
9.3
DANN
Benign
0.78

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1755271; hg19: chr9-17979578; API