rs3776817

chr5-179152747-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014244.5(ADAMTS2):c.1516-492G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,882 control chromosomes in the GnomAD database, including 6,288 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 0.28 (6288 hom., cov: 32)
• Consequence: ADAMTS2 NM_014244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

Genes affected

ADAMTS2 (HGNC:218): (ADAM metallopeptidase with thrombospondin type 1 motif 2) This gene encodes a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) protein family. Members of the family share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. Individual members of this family differ in the number of C-terminal TS motifs, and some have unique C-terminal domains. The encoded preproprotein is proteolytically processed to generate the mature procollagen N-proteinase. This proteinase excises the N-propeptide of the fibrillar procollagens types I-III and type V. Mutations in this gene cause Ehlers-Danlos syndrome type VIIC, a recessively inherited connective-tissue disorder. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTS2	NM_014244.5	c.1516-492G>A		intron_variant		ENST00000251582.12
ADAMTS2	NM_021599.4	c.1516-492G>A		intron_variant
ADAMTS2	XM_047417895.1	c.1021-492G>A		intron_variant
ADAMTS2	XM_047417896.1	c.634-492G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTS2	ENST00000251582.12	c.1516-492G>A		intron_variant		1	NM_014244.5	P2
ADAMTS2	ENST00000274609.5	c.1516-492G>A		intron_variant		1
ADAMTS2	ENST00000518335.3	c.1516-492G>A		intron_variant		3		A2
ADAMTS2	ENST00000698889.1	c.1516-492G>A		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43178 AN: 151764 Hom.: 6268 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.285 AC: 43236 AN: 151882 Hom.: 6288 Cov.: 32 AF XY: 0.286 AC XY: 21241 AN XY: 74218

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.289

Alfa AF: 0.255 Hom.: 2369

Bravo AF: 0.295

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.8
Dann	Benign	0.56

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

Publications

LitVar

Other links and lift over

dbSNP: rs3776817; hg19: chr5-178579748;