NM_025003.5:c.1117+1697G>A

Variant names:

• chr12-43488698-C-T
• rs1510523
• NM_025003.5:c.1117+1697G>A

Variant summary

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

The NM_025003.5(ADAMTS20):​c.1117+1697G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,966 control chromosomes in the GnomAD database, including 8,889 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 0.33 (8889 hom., cov: 32)
• Consequence: ADAMTS20 NM_025003.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490
• Publications: 2 publications found

Genes affected

ADAMTS20 (HGNC:17178): (ADAM metallopeptidase with thrombospondin type 1 motif 20) The protein encoded by this gene is a member of the ADAMTS family of zinc-dependent proteases. The encoded protein has a signal peptide that is cleaved to release the mature peptide, which is secreted and found in the extracellular matrix. This protein may be involved in tissue remodeling. [provided by RefSeq, Sep 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025003.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS20	NM_025003.5	MANE Select	c.1117+1697G>A		intron	N/A	NP_079279.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS20	ENST00000389420.8	TSL:1 MANE Select	c.1117+1697G>A		intron	N/A	ENSP00000374071.3
	ADAMTS20	ENST00000553158.5	TSL:5	c.1117+1697G>A		intron	N/A	ENSP00000448341.1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50084 AN: 151848 Hom.: 8881 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.330 AC: 50113 AN: 151966 Hom.: 8889 Cov.: 32 AF XY: 0.337 AC XY: 25013 AN XY: 74308

African (AFR) AF: 0.257 AC: 10650 AN: 41462

American (AMR) AF: 0.338 AC: 5155 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1288 AN: 3470

East Asian (EAS) AF: 0.753 AC: 3899 AN: 5180

South Asian (SAS) AF: 0.501 AC: 2416 AN: 4826

European-Finnish (FIN) AF: 0.313 AC: 3304 AN: 10548

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22285 AN: 67906

Other (OTH) AF: 0.362 AC: 763 AN: 2106

Alfa AF: 0.184 Hom.: 380

Bravo AF: 0.330

Asia WGS AF: 0.618 AC: 2148 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.1
DANN	Benign	0.64
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1510523; hg19: chr12-43882501;