Genetic Variant THBS2:p.Pro1089Leu (chr6-169222204-G-A) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_003247.5(THBS2):c.3266C>T(p.Pro1089Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00082 in 1,604,894 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0013 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00077 ( 3 hom. )

Consequence

THBS2
NM_003247.5 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.82

Variant links:

Genes affected

THBS2 (HGNC:11786): (thrombospondin 2) The protein encoded by this gene belongs to the thrombospondin family. It is a disulfide-linked homotrimeric glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. This protein has been shown to function as a potent inhibitor of tumor growth and angiogenesis. Studies of the mouse counterpart suggest that this protein may modulate the cell surface properties of mesenchymal cells and be involved in cell adhesion and migration. [provided by RefSeq, Jul 2008]

THBS2 links:

THBS2-AS1 (HGNC:56059): (THBS2 antisense RNA 1)

THBS2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.013661802).

BP6

Variant 6-169222204-G-A is Benign according to our data. Variant chr6-169222204-G-A is described in ClinVar as [Benign]. Clinvar id is 3034072.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High AC in GnomAd4 at 204 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THBS2	NM_003247.5 link	c.3266C>T	p.Pro1089Leu	missense_variant	Exon 19 of 22	ENST00000617924.6	NP_003238.2	P35442

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THBS2	ENST00000617924.6 link	c.3266C>T	p.Pro1089Leu	missense_variant	Exon 19 of 22	1	NM_003247.5	ENSP00000482784.1		P35442

Frequencies

GnomAD3 genomes

AF:

0.00133

AC:

203

AN:

152170

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000196

Gnomad ASJ

AF:

0.00980

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0115

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000603

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00141

AC:

343

AN:

243860

Hom.:

AF XY:

0.00138

AC XY:

182

AN XY:

132300

show subpopulations

Gnomad AFR exome

AF:

0.0000622

Gnomad AMR exome

AF:

0.000175

Gnomad ASJ exome

AF:

0.00715

Gnomad EAS exome

AF:

0.0000547

Gnomad SAS exome

AF:

0.0000665

Gnomad FIN exome

AF:

0.00834

Gnomad NFE exome

AF:

0.000804

Gnomad OTH exome

AF:

0.00166

GnomAD4 exome

AF:

0.000766

AC:

1112

AN:

1452606

Hom.:

Cov.:

AF XY:

0.000770

AC XY:

556

AN XY:

721920

show subpopulations

Gnomad4 AFR exome

AF:

0.0000899

Gnomad4 AMR exome

AF:

0.000112

Gnomad4 ASJ exome

AF:

0.00730

Gnomad4 EAS exome

AF:

0.000708

Gnomad4 SAS exome

AF:

0.0000233

Gnomad4 FIN exome

AF:

0.00777

Gnomad4 NFE exome

AF:

0.000376

Gnomad4 OTH exome

AF:

0.00117

GnomAD4 genome

AF:

0.00134

AC:

204

AN:

152288

Hom.:

Cov.:

AF XY:

0.00189

AC XY:

141

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0000481

Gnomad4 AMR

AF:

0.000196

Gnomad4 ASJ

AF:

0.00980

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0115

Gnomad4 NFE

AF:

0.000603

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000871

Hom.:

Bravo

AF:

0.000506

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.000814

AC:

ExAC

AF:

0.00137

AC:

166

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

THBS2-related disorder

Benign:1

Jan 21, 2020

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.29

BayesDel_noAF

Benign

-0.27

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Uncertain

0.66

D;.;D

Eigen

Benign

-0.60

Eigen_PC

Benign

-0.74

FATHMM_MKL

Benign

0.14

LIST_S2

Benign

0.85

.;T;T

M_CAP

Benign

0.046

MetaRNN

Benign

0.014

T;T;T

MetaSVM

Uncertain

-0.18

MutationAssessor

Benign

2.0

M;.;M

PrimateAI

Benign

0.40

PROVEAN

Pathogenic

-4.4

D;.;.

REVEL

Benign

0.28

Sift

Uncertain

0.010

D;.;.

Sift4G

Uncertain

0.035

D;.;D

Polyphen

0.59

P;.;P

Vest4

0.29

MVP

0.83

MPC

0.55

ClinPred

0.071

GERP RS

1.8

Varity_R

0.086

gMVP

0.22

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