Genetic Variant EXT2:p.Arg10Arg (chr11-44107740-C-A) – ACMG Classification: Benign (-17 pts)

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4BP6_Very_StrongBA1

The NM_207122.2(EXT2):c.28C>A(p.Arg10Arg) variant causes a synonymous change. The variant allele was found at a frequency of 0.0156 in 1,614,126 control chromosomes in the GnomAD database, including 1,714 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 240 hom., cov: 32)

Exomes 𝑓: 0.015 ( 1474 hom. )

Consequence

EXT2
NM_207122.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 5.73

Variant links:

Genes affected

EXT2 (HGNC:3513): (exostosin glycosyltransferase 2) This gene encodes one of two glycosyltransferases involved in the chain elongation step of heparan sulfate biosynthesis. Mutations in this gene cause the type II form of multiple exostoses. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jul 2008]

EXT2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.16).

BP6

Variant 11-44107740-C-A is Benign according to our data. Variant chr11-44107740-C-A is described in ClinVar as [Benign]. Clinvar id is 195445.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-44107740-C-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EXT2	NM_207122.2 link	c.28C>A	p.Arg10Arg	synonymous_variant	Exon 2 of 14	ENST00000533608.7	NP_997005.1	Q93063-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EXT2	ENST00000533608.7 link	c.28C>A	p.Arg10Arg	synonymous_variant	Exon 2 of 14	1	NM_207122.2	ENSP00000431173.2		Q93063-1

Frequencies

GnomAD3 genomes

AF:

0.0192

AC:

2925

AN:

152134

Hom.:

242

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00454

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0315

Gnomad ASJ

AF:

0.00577

Gnomad EAS

AF:

0.280

Gnomad SAS

AF:

0.0599

Gnomad FIN

AF:

0.0157

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00447

Gnomad OTH

AF:

0.0120

GnomAD3 exomes

AF:

0.0354

AC:

8899

AN:

251388

Hom.:

797

AF XY:

0.0343

AC XY:

4667

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.00511

Gnomad AMR exome

AF:

0.0355

Gnomad ASJ exome

AF:

0.00714

Gnomad EAS exome

AF:

0.282

Gnomad SAS exome

AF:

0.0458

Gnomad FIN exome

AF:

0.0150

Gnomad NFE exome

AF:

0.00432

Gnomad OTH exome

AF:

0.0186

GnomAD4 exome

AF:

0.0153

AC:

22314

AN:

1461874

Hom.:

1474

Cov.:

AF XY:

0.0161

AC XY:

11688

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00349

Gnomad4 AMR exome

AF:

0.0353

Gnomad4 ASJ exome

AF:

0.00627

Gnomad4 EAS exome

AF:

0.251

Gnomad4 SAS exome

AF:

0.0455

Gnomad4 FIN exome

AF:

0.0148

Gnomad4 NFE exome

AF:

0.00401

Gnomad4 OTH exome

AF:

0.0216

GnomAD4 genome

AF:

0.0192

AC:

2925

AN:

152252

Hom.:

240

Cov.:

AF XY:

0.0219

AC XY:

1627

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.00452

Gnomad4 AMR

AF:

0.0316

Gnomad4 ASJ

AF:

0.00577

Gnomad4 EAS

AF:

0.280

Gnomad4 SAS

AF:

0.0603

Gnomad4 FIN

AF:

0.0157

Gnomad4 NFE

AF:

0.00447

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.00814

Hom.:

141

Bravo

AF:

0.0208

Asia WGS

AF:

0.132

AC:

457

AN:

3478

EpiCase

AF:

0.00463

EpiControl

AF:

0.00379

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Exostoses, multiple, type 2

Benign:3

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 01, 2025

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:2

Oct 20, 2014

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Exostoses, multiple, type 1

Benign:1

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.16

CADD

Benign

DANN

Benign

0.67

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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