9-17907830-A-T

Variant names:

• chr9-17907830-A-T
• rs1343844
• ENST00000680146.1:c.87+908A>T

Variant summary

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

The ENST00000680146.1(ADAMTSL1):​c.87+908A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,036 control chromosomes in the GnomAD database, including 2,094 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 0.16 (2094 hom., cov: 31)
• Consequence: ADAMTSL1 ENST00000680146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTSL1	XM_011518063.3	c.22+363A>T		intron_variant	Intron 1 of 30		XP_011516365.1
ADAMTSL1	XM_011518064.4	c.96+908A>T		intron_variant	Intron 1 of 29		XP_011516366.1
ADAMTSL1	XM_017015311.2	c.22+363A>T		intron_variant	Intron 1 of 29		XP_016870800.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTSL1	ENST00000680146.1	c.87+908A>T		intron_variant	Intron 1 of 29			ENSP00000505591.1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24170 AN: 151918 Hom.: 2093 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0217

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.159 AC: 24204 AN: 152036 Hom.: 2094 Cov.: 31 AF XY: 0.155 AC XY: 11530 AN XY: 74346

African (AFR) AF: 0.218 AC: 9027 AN: 41452

American (AMR) AF: 0.140 AC: 2147 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3472

East Asian (EAS) AF: 0.0219 AC: 113 AN: 5154

South Asian (SAS) AF: 0.128 AC: 618 AN: 4810

European-Finnish (FIN) AF: 0.123 AC: 1300 AN: 10586

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9938 AN: 67958

Other (OTH) AF: 0.164 AC: 345 AN: 2110

Alfa AF: 0.0557 Hom.: 65

Bravo AF: 0.163

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.69
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1343844; hg19: chr9-17907828;