chr9-18622045-T-G

Position:

• chr9-18622045-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040272.6(ADAMTSL1):​c.475-198T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,158 control chromosomes in the GnomAD database, including 1,543 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 0.14 (1543 hom., cov: 32)
• Consequence: ADAMTSL1 NM_001040272.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTSL1	NM_001040272.6	c.475-198T>G		intron_variant		ENST00000380548.9	NP_001035362.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAMTSL1	ENST00000380548.9	c.475-198T>G		intron_variant		5	NM_001040272.6	ENSP00000369921	P1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20845 AN: 152040 Hom.: 1543 Cov.: 32

Gnomad AFR AF: 0.0921

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.137 AC: 20858 AN: 152158 Hom.: 1543 Cov.: 32 AF XY: 0.137 AC XY: 10180 AN XY: 74382

Gnomad4 AFR AF: 0.0922

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.141

Alfa AF: 0.150 Hom.: 3610

Bravo AF: 0.134

Asia WGS AF: 0.167 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.094
DANN	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10963676; hg19: chr9-18622043;