ENST00000680146.1:c.87+908A>T

Variant names:

• chr9-17907830-A-T
• rs1343844
• ENST00000680146.1:c.87+908A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000680146.1(ADAMTSL1):​c.87+908A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,036 control chromosomes in the GnomAD database, including 2,094 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 0.16 (2094 hom., cov: 31)
• Consequence: ADAMTSL1 ENST00000680146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 7 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL1	ENST00000680146.1		c.87+908A>T		intron	N/A	ENSP00000505591.1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24170 AN: 151918 Hom.: 2093 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0217

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.159 AC: 24204 AN: 152036 Hom.: 2094 Cov.: 31 AF XY: 0.155 AC XY: 11530 AN XY: 74346

African (AFR) AF: 0.218 AC: 9027 AN: 41452

American (AMR) AF: 0.140 AC: 2147 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3472

East Asian (EAS) AF: 0.0219 AC: 113 AN: 5154

South Asian (SAS) AF: 0.128 AC: 618 AN: 4810

European-Finnish (FIN) AF: 0.123 AC: 1300 AN: 10586

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9938 AN: 67958

Other (OTH) AF: 0.164 AC: 345 AN: 2110

Alfa AF: 0.0557 Hom.: 65

Bravo AF: 0.163

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.69
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1343844; hg19: chr9-17907828;