chr9-17938353-T-C

Variant names:

• chr9-17938353-T-C
• rs1755289
• ENST00000680146.1:c.87+31431T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000680146.1(ADAMTSL1):​c.87+31431T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,882 control chromosomes in the GnomAD database, including 23,451 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 0.54 (23451 hom., cov: 31)
• Consequence: ADAMTSL1 ENST00000680146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.909
• Publications: 16 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000680146.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL1	ENST00000680146.1		c.87+31431T>C		intron	N/A	ENSP00000505591.1	A0A7P0T9B9

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81870 AN: 151764 Hom.: 23445 Cov.: 31

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.560

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.539 AC: 81888 AN: 151882 Hom.: 23451 Cov.: 31 AF XY: 0.543 AC XY: 40280 AN XY: 74176

African (AFR) AF: 0.330 AC: 13688 AN: 41434

American (AMR) AF: 0.617 AC: 9416 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2088 AN: 3466

East Asian (EAS) AF: 0.591 AC: 3018 AN: 5110

South Asian (SAS) AF: 0.555 AC: 2670 AN: 4810

European-Finnish (FIN) AF: 0.665 AC: 7017 AN: 10550

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.619 AC: 42078 AN: 67948

Other (OTH) AF: 0.558 AC: 1177 AN: 2110

Alfa AF: 0.586 Hom.: 89394

Bravo AF: 0.526

Asia WGS AF: 0.537 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	17
DANN	Benign	0.55
PhyloP100		0.91

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1755289;

hg19: chr9-17938351;