ENST00000680146.1:c.207+156778C>T

Variant names:

• chr9-18320759-C-T
• rs10115405
• ENST00000680146.1:c.207+156778C>T

Variant summary

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

The ENST00000680146.1(ADAMTSL1):​c.207+156778C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,882 control chromosomes in the GnomAD database, including 20,560 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 0.52 (20560 hom., cov: 32)
• Consequence: ADAMTSL1 ENST00000680146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.613 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.207+156778C>T		intron	N/A	ENSP00000505591.1

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78199 AN: 151760 Hom.: 20533 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.515 AC: 78271 AN: 151882 Hom.: 20560 Cov.: 32 AF XY: 0.516 AC XY: 38287 AN XY: 74220

African (AFR) AF: 0.575 AC: 23829 AN: 41420

American (AMR) AF: 0.624 AC: 9521 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2042 AN: 5164

South Asian (SAS) AF: 0.486 AC: 2340 AN: 4814

European-Finnish (FIN) AF: 0.478 AC: 5026 AN: 10522

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.476 AC: 32310 AN: 67922

Other (OTH) AF: 0.508 AC: 1069 AN: 2106

Alfa AF: 0.434 Hom.: 1636

Bravo AF: 0.531

Asia WGS AF: 0.492 AC: 1701 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.20
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10115405; hg19: chr9-18320757;