rs10810961

Positions:

• chr9-18371968-A-G
• chr9-18371968-A-T

Variant summary

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

The XR_001746428.1(LOC107986990):​n.9392-8855A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0944 in 152,294 control chromosomes in the GnomAD database, including 945 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 0.094 (945 hom., cov: 32)
• Consequence: LOC107986990 XR_001746428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

Genes affected

LOC107986990 (HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986990	XR_001746428.1	n.9392-8855A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAMTSL1	ENST00000680146.1	c.208-132861A>G		intron_variant				ENSP00000505591

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14361 AN: 152176 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0944 AC: 14373 AN: 152294 Hom.: 945 Cov.: 32 AF XY: 0.0932 AC XY: 6938 AN XY: 74462

Gnomad4 AFR AF: 0.0402

Gnomad4 AMR AF: 0.0901

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.0431

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.116

Alfa AF: 0.108 Hom.: 1394

Bravo AF: 0.0924

Asia WGS AF: 0.232 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.34
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10810961; hg19: chr9-18371966;