rs3124767

chr9-133443421-T-Cchr9-133443421-T-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_139027.6(ADAMTS13):c.2280T>C(p.Gly760=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 1,595,854 control chromosomes in the GnomAD database, including 267,720 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.58 (26927 hom., cov: 33)
  • Exomes 𝑓: 0.57 (240793 hom.)
• Consequence: ADAMTS13 NM_139027.6 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.49

Genes affected

ADAMTS13 (HGNC:1366): (ADAM metallopeptidase with thrombospondin type 1 motif 13) This gene encodes a member of a family of proteins containing several distinct regions, including a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. The enzyme encoded by this gene specifically cleaves von Willebrand Factor (vWF). Defects in this gene are associated with thrombotic thrombocytopenic purpura. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 9-133443421-T-C is Benign according to our data. Variant chr9-133443421-T-C is described in ClinVar as [Benign]. Clinvar id is 769360.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-4.49 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTS13	NM_139027.6	c.2280T>C	p.Gly760=	synonymous_variant	19/29	ENST00000355699.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTS13	ENST00000355699.7	c.2280T>C	p.Gly760=	synonymous_variant	19/29	1	NM_139027.6	A2

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88886 AN: 151996 Hom.: 26882 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.533

GnomAD4 exome AF: 0.571 AC: 824762 AN: 1443740 Hom.: 240793 Cov.: 77 AF XY: 0.569 AC XY: 408243 AN XY: 717788

Gnomad4 AFR exome AF: 0.677

Gnomad4 AMR exome AF: 0.487

Gnomad4 ASJ exome AF: 0.387

Gnomad4 EAS exome AF: 0.199

Gnomad4 SAS exome AF: 0.504

Gnomad4 FIN exome AF: 0.673

Gnomad4 NFE exome AF: 0.592

Gnomad4 OTH exome AF: 0.547

GnomAD4 genome AF: 0.585 AC: 88982 AN: 152114 Hom.: 26927 Cov.: 33 AF XY: 0.583 AC XY: 43385 AN XY: 74366

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.528

Alfa AF: 0.576 Hom.: 7237

Bravo AF: 0.571

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.037

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3124767; hg19: chr9-136308542;