9-18142900-T-G

Variant names:

• chr9-18142900-T-G
• rs7849137
• ENST00000680146.1:c.88-20962T>G

Variant summary

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

The ENST00000680146.1(ADAMTSL1):​c.88-20962T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,058 control chromosomes in the GnomAD database, including 39,560 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 0.71 (39560 hom., cov: 32)
• Consequence: ADAMTSL1 ENST00000680146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 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.88-20962T>G		intron	N/A	ENSP00000505591.1

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108193 AN: 151938 Hom.: 39550 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.712 AC: 108247 AN: 152058 Hom.: 39560 Cov.: 32 AF XY: 0.712 AC XY: 52928 AN XY: 74332

African (AFR) AF: 0.524 AC: 21699 AN: 41436

American (AMR) AF: 0.772 AC: 11794 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2808 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3370 AN: 5158

South Asian (SAS) AF: 0.777 AC: 3752 AN: 4828

European-Finnish (FIN) AF: 0.771 AC: 8156 AN: 10578

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54249 AN: 67988

Other (OTH) AF: 0.741 AC: 1564 AN: 2112

Alfa AF: 0.772 Hom.: 59157

Bravo AF: 0.701

Asia WGS AF: 0.720 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.70
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs7849137; hg19: chr9-18142898;