rs7862683

Variant names:

• chr9-18267949-C-G
• rs7862683
• ENST00000680146.1:c.207+103968C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-18267949-C-G
• chr9-18267949-C-T

Variant summary

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

The ENST00000680146.1(ADAMTSL1):​c.207+103968C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,692 control chromosomes in the GnomAD database, including 10,809 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 0.36 (10809 hom., cov: 31)
• Consequence: ADAMTSL1 ENST00000680146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.491 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+103968C>G		intron	N/A	ENSP00000505591.1	A0A7P0T9B9

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54760 AN: 151574 Hom.: 10811 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.361 AC: 54763 AN: 151692 Hom.: 10809 Cov.: 31 AF XY: 0.363 AC XY: 26877 AN XY: 74128

African (AFR) AF: 0.220 AC: 9110 AN: 41372

American (AMR) AF: 0.274 AC: 4176 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1640 AN: 3472

East Asian (EAS) AF: 0.264 AC: 1361 AN: 5156

South Asian (SAS) AF: 0.507 AC: 2449 AN: 4828

European-Finnish (FIN) AF: 0.481 AC: 5042 AN: 10488

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29788 AN: 67836

Other (OTH) AF: 0.361 AC: 760 AN: 2108

Alfa AF: 0.244 Hom.: 633

Bravo AF: 0.332

Asia WGS AF: 0.387 AC: 1333 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.36
PhyloP100		0.46

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7862683;

hg19: chr9-18267947;