Variant 15-100109160-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_139057.4(ADAMTS17):c.1889-44G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0128 in 1,572,098 control chromosomes in the GnomAD database, including 475 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0080 ( 26 hom., cov: 33)

Exomes 𝑓: 0.013 ( 449 hom. )

Consequence

ADAMTS17
NM_139057.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.570

Variant links:

Genes affected

ADAMTS17 (HGNC:17109): (ADAM metallopeptidase with thrombospondin type 1 motif 17) This gene encodes a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) protein family. ADAMTS family members 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 protein, which may promote breast cancer cell growth and survival. Mutations in this gene are associated with a Weill-Marchesani-like syndrome, which is characterized by lenticular myopia, ectopia lentis, glaucoma, spherophakia, and short stature. [provided by RefSeq, May 2016]

ADAMTS17 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 15-100109160-C-T is Benign according to our data. Variant chr15-100109160-C-T is described in ClinVar as [Benign]. Clinvar id is 1279433.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTS17	NM_139057.4 linkuse as main transcript	c.1889-44G>A		intron_variant		ENST00000268070.9	NP_620688.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
ADAMTS17	ENST00000268070.9 linkuse as main transcript	c.1889-44G>A	intron_variant	1	NM_139057.4	ENSP00000268070		Q8TE56-1
ADAMTS17	ENST00000568565.2 linkuse as main transcript	c.1889-44G>A	intron_variant	5		ENSP00000456161	P1
ADAMTS17	ENST00000378898.8 linkuse as main transcript	n.1570-44G>A	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00802

AC:

1220

AN:

152062

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00164

Gnomad ASJ

AF:

0.000866

Gnomad EAS

AF:

0.000965

Gnomad SAS

AF:

0.100

Gnomad FIN

AF:

0.00283

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00862

Gnomad OTH

AF:

0.0115

GnomAD3 exomes

AF:

0.0178

AC:

3198

AN:

179460

Hom.:

141

AF XY:

0.0228

AC XY:

2188

AN XY:

95960

show subpopulations

Gnomad AFR exome

AF:

0.00174

Gnomad AMR exome

AF:

0.00147

Gnomad ASJ exome

AF:

0.00103

Gnomad EAS exome

AF:

0.00217

Gnomad SAS exome

AF:

0.0941

Gnomad FIN exome

AF:

0.00232

Gnomad NFE exome

AF:

0.00866

Gnomad OTH exome

AF:

0.0105

GnomAD4 exome

AF:

0.0133

AC:

18876

AN:

1419918

Hom.:

449

Cov.:

AF XY:

0.0157

AC XY:

11008

AN XY:

702756

show subpopulations

Gnomad4 AFR exome

AF:

0.00179

Gnomad4 AMR exome

AF:

0.00169

Gnomad4 ASJ exome

AF:

0.00126

Gnomad4 EAS exome

AF:

0.000808

Gnomad4 SAS exome

AF:

0.0892

Gnomad4 FIN exome

AF:

0.00261

Gnomad4 NFE exome

AF:

0.00950

Gnomad4 OTH exome

AF:

0.0135

GnomAD4 genome

AF:

0.00801

AC:

1219

AN:

152180

Hom.:

Cov.:

AF XY:

0.00915

AC XY:

681

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.00145

Gnomad4 AMR

AF:

0.00164

Gnomad4 ASJ

AF:

0.000866

Gnomad4 EAS

AF:

0.000967

Gnomad4 SAS

AF:

0.101

Gnomad4 FIN

AF:

0.00283

Gnomad4 NFE

AF:

0.00862

Gnomad4 OTH

AF:

0.0114

Alfa

AF:

0.00450

Hom.:

Bravo

AF:

0.00524

Asia WGS

AF:

0.0530

AC:

185

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 08, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.18

DANN

Benign

0.67

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over