rs11037882

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_207122.2(EXT2):c.1080-18T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 1,601,054 control chromosomes in the GnomAD database, including 82,186 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6498 hom., cov: 32)

Exomes 𝑓: 0.31 ( 75688 hom. )

Consequence

EXT2
NM_207122.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.363

Publications

12 publications found

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 Gene-Disease associations (from GenCC):

exostoses, multiple, type 2
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, G2P
seizures-scoliosis-macrocephaly syndrome
Inheritance: AR Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet
hereditary multiple osteochondromas
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

EXT2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 11-44130027-T-A is Benign according to our data. Variant chr11-44130027-T-A is described in ClinVar as Benign. ClinVar VariationId is 198636.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EXT2	NM_207122.2 link	c.1080-18T>A		intron_variant	Intron 6 of 13	ENST00000533608.7	NP_997005.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EXT2	ENST00000533608.7 link	c.1080-18T>A		intron_variant	Intron 6 of 13	1	NM_207122.2	ENSP00000431173.2

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40838

AN:

151934

Hom.:

6478

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.382

Gnomad AMR

AF:

0.447

Gnomad ASJ

AF:

0.223

Gnomad EAS

AF:

0.438

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.287

GnomAD2 exomes

AF:

0.343

AC:

86193

AN:

251202

AF XY:

0.338

show subpopulations

Gnomad AFR exome

AF:

0.116

Gnomad AMR exome

AF:

0.589

Gnomad ASJ exome

AF:

0.222

Gnomad EAS exome

AF:

0.458

Gnomad FIN exome

AF:

0.323

Gnomad NFE exome

AF:

0.286

Gnomad OTH exome

AF:

0.320

GnomAD4 exome

AF:

0.314

AC:

454857

AN:

1449002

Hom.:

75688

Cov.:

AF XY:

0.315

AC XY:

227214

AN XY:

721714

show subpopulations

African (AFR)

AF:

0.108

AC:

3582

AN:

33228

American (AMR)

AF:

0.572

AC:

25575

AN:

44692

Ashkenazi Jewish (ASJ)

AF:

0.216

AC:

5618

AN:

26064

East Asian (EAS)

AF:

0.434

AC:

17204

AN:

39622

South Asian (SAS)

AF:

0.387

AC:

33262

AN:

85984

European-Finnish (FIN)

AF:

0.313

AC:

16698

AN:

53402

Middle Eastern (MID)

AF:

0.227

AC:

1306

AN:

5754

European-Non Finnish (NFE)

AF:

0.303

AC:

333449

AN:

1100282

Other (OTH)

AF:

0.303

AC:

18163

AN:

59974

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

14332

28664

42995

57327

71659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11212

22424

33636

44848

56060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.269

AC:

40873

AN:

152052

Hom.:

6498

Cov.:

AF XY:

0.276

AC XY:

20487

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.122

AC:

5048

AN:

41494

American (AMR)

AF:

0.448

AC:

6844

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.223

AC:

773

AN:

3468

East Asian (EAS)

AF:

0.436

AC:

2250

AN:

5158

South Asian (SAS)

AF:

0.378

AC:

1819

AN:

4814

European-Finnish (FIN)

AF:

0.317

AC:

3349

AN:

10562

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.291

AC:

19768

AN:

67964

Other (OTH)

AF:

0.295

AC:

622

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1447

2894

4342

5789

7236

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

414

828

1242

1656

2070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.265

Hom.:

1092

Bravo

AF:

0.273

Asia WGS

AF:

0.448

AC:

1555

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Jul 17, 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

- -

Exostoses, multiple, type 2

Benign:2

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Aug 10, 2021

Genome-Nilou Lab

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

- -

Seizures-scoliosis-macrocephaly syndrome

Benign:1

Aug 10, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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

-0.58

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

0.36

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over