rs6475216

Variant names:

• chr9-18444140-C-T
• rs6475216
• ENST00000680146.1:c.208-60689C>T

Variant summary

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

The ENST00000680146.1(ADAMTSL1):​c.208-60689C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,996 control chromosomes in the GnomAD database, including 19,321 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 0.50 (19321 hom., cov: 33)
• Consequence: ADAMTSL1 ENST00000680146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 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.208-60689C>T		intron	N/A	ENSP00000505591.1	A0A7P0T9B9

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75394 AN: 151878 Hom.: 19312 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.496 AC: 75426 AN: 151996 Hom.: 19321 Cov.: 33 AF XY: 0.502 AC XY: 37277 AN XY: 74310

African (AFR) AF: 0.360 AC: 14935 AN: 41458

American (AMR) AF: 0.478 AC: 7295 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1846 AN: 3464

East Asian (EAS) AF: 0.544 AC: 2811 AN: 5170

South Asian (SAS) AF: 0.454 AC: 2187 AN: 4816

European-Finnish (FIN) AF: 0.629 AC: 6656 AN: 10582

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37973 AN: 67926

Other (OTH) AF: 0.491 AC: 1033 AN: 2104

Alfa AF: 0.536 Hom.: 83190

Bravo AF: 0.481

Asia WGS AF: 0.447 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.45
PhyloP100		0.021

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: rs6475216;

hg19: chr9-18444138;