rs16936441

Variant names:

• chr9-18211657-G-A
• rs16936441
• ENST00000680146.1:c.207+47676G>A

Variant summary

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

The ENST00000680146.1(ADAMTSL1):​c.207+47676G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,008 control chromosomes in the GnomAD database, including 2,358 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 0.17 (2358 hom., cov: 32)
• Consequence: ADAMTSL1 ENST00000680146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL1	ENST00000680146.1		c.207+47676G>A		intron	N/A	ENSP00000505591.1	A0A7P0T9B9

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26099 AN: 151890 Hom.: 2355 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.172 AC: 26120 AN: 152008 Hom.: 2358 Cov.: 32 AF XY: 0.169 AC XY: 12525 AN XY: 74300

African (AFR) AF: 0.126 AC: 5217 AN: 41482

American (AMR) AF: 0.153 AC: 2343 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1280 AN: 5162

South Asian (SAS) AF: 0.175 AC: 845 AN: 4816

European-Finnish (FIN) AF: 0.148 AC: 1560 AN: 10576

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13530 AN: 67930

Other (OTH) AF: 0.190 AC: 399 AN: 2098

Alfa AF: 0.179 Hom.: 1128

Bravo AF: 0.171

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.5
DANN	Benign	0.52
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs16936441; hg19: chr9-18211655;