ENST00000680146.1:c.87+72658T>C

Variant names:

• chr9-17979580-T-C
• rs1755271
• ENST00000680146.1:c.87+72658T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL1	ENST00000680146.1		c.87+72658T>C		intron	N/A	ENSP00000505591.1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80211 AN: 151086 Hom.: 23062 Cov.: 29

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

African (AFR) AF: 0.308 AC: 12705 AN: 41244

American (AMR) AF: 0.622 AC: 9461 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1751 AN: 3464

East Asian (EAS) AF: 0.921 AC: 4682 AN: 5086

South Asian (SAS) AF: 0.604 AC: 2887 AN: 4782

European-Finnish (FIN) AF: 0.585 AC: 6089 AN: 10400

Middle Eastern (MID) AF: 0.417 AC: 121 AN: 290

European-Non Finnish (NFE) AF: 0.604 AC: 40901 AN: 67728

Other (OTH) AF: 0.528 AC: 1111 AN: 2106

Alfa AF: 0.577 Hom.: 55210

Bravo AF: 0.529

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.3
DANN	Benign	0.78
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1755271; hg19: chr9-17979578;