19-8580465-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_030957.4(ADAMTS10):c.*428A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0662 in 169,020 control chromosomes in the GnomAD database, including 1,156 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.073 (1149 hom., cov: 30)
  • Exomes 𝑓: 0.0074 (7 hom.)
• Consequence: ADAMTS10 NM_030957.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.338

Genes affected

ADAMTS10 (HGNC:13201): (ADAM metallopeptidase with thrombospondin type 1 motif 10) This gene belongs to the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 motifs) family of zinc-dependent proteases. ADAMTS proteases are complex secreted enzymes containing a prometalloprotease domain of the reprolysin type attached to an ancillary domain with a highly conserved structure that includes at least one thrombospondin type 1 repeat. They have been demonstrated to have important roles in connective tissue organization, coagulation, inflammation, arthritis, angiogenesis and cell migration. The product of this gene plays a major role in growth and in skin, lens, and heart development. It is also a candidate gene for autosomal recessive Weill-Marchesani syndrome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 19-8580465-T-C is Benign according to our data. Variant chr19-8580465-T-C is described in ClinVar as [Benign]. Clinvar id is 330569.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTS10	NM_030957.4	c.*428A>G		3_prime_UTR_variant	26/26	ENST00000597188.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTS10	ENST00000597188.6	c.*428A>G		3_prime_UTR_variant	26/26	5	NM_030957.4	P1
ADAMTS10	ENST00000270328.8	c.*428A>G		3_prime_UTR_variant	25/25	5		P1
ADAMTS10	ENST00000595838.5	c.*428A>G		3_prime_UTR_variant	13/13	2

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11021 AN: 150728 Hom.: 1149 Cov.: 30

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0310

Gnomad ASJ AF: 0.0177

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.00670

Gnomad FIN AF: 0.00250

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0545

GnomAD4 exome AF: 0.00737 AC: 134 AN: 18176 Hom.: 7 Cov.: 0 AF XY: 0.00745 AC XY: 79 AN XY: 10608

Gnomad4 AFR exome AF: 0.161

Gnomad4 AMR exome AF: 0.0189

Gnomad4 ASJ exome AF: 0.00368

Gnomad4 EAS exome AF: 0.00313

Gnomad4 SAS exome AF: 0.00375

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00485

Gnomad4 OTH exome AF: 0.00756

GnomAD4 genome AF: 0.0733 AC: 11050 AN: 150844 Hom.: 1149 Cov.: 30 AF XY: 0.0717 AC XY: 5289 AN XY: 73754

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0177

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.00650

Gnomad4 FIN AF: 0.00250

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.0563

Alfa AF: 0.00642 Hom.: 7

Bravo AF: 0.0831

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Weill-Marchesani syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.8
Dann	Benign	0.66

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: rs116024095; hg19: chr19-8645349;