dbSNP rs11037909: EXT2:c.1807-51T>C (chr11-44234064-T-C) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_207122.2(EXT2):c.1807-51T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 1,611,356 control chromosomes in the GnomAD database, including 72,112 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5937 hom., cov: 32)

Exomes 𝑓: 0.29 ( 66175 hom. )

Consequence

EXT2
NM_207122.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.957

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 11-44234064-T-C is Benign according to our data. Variant chr11-44234064-T-C is described in ClinVar as [Benign]. Clinvar id is 1166104.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-44234064-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EXT2	NM_207122.2 link	c.1807-51T>C		intron_variant	Intron 11 of 13	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.1807-51T>C		intron_variant	Intron 11 of 13	1	NM_207122.2	ENSP00000431173.2		Q93063-1

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39596

AN:

152038

Hom.:

5917

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.335

Gnomad AMR

AF:

0.417

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.414

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.267

GnomAD3 exomes

AF:

0.321

AC:

80056

AN:

249572

Hom.:

14574

AF XY:

0.317

AC XY:

42767

AN XY:

135008

show subpopulations

Gnomad AFR exome

AF:

0.140

Gnomad AMR exome

AF:

0.534

Gnomad ASJ exome

AF:

0.197

Gnomad EAS exome

AF:

0.433

Gnomad SAS exome

AF:

0.370

Gnomad FIN exome

AF:

0.319

Gnomad NFE exome

AF:

0.263

Gnomad OTH exome

AF:

0.297

GnomAD4 exome

AF:

0.293

AC:

427449

AN:

1459200

Hom.:

66175

Cov.:

AF XY:

0.294

AC XY:

213263

AN XY:

725990

show subpopulations

Gnomad4 AFR exome

AF:

0.133

Gnomad4 AMR exome

AF:

0.521

Gnomad4 ASJ exome

AF:

0.191

Gnomad4 EAS exome

AF:

0.394

Gnomad4 SAS exome

AF:

0.368

Gnomad4 FIN exome

AF:

0.307

Gnomad4 NFE exome

AF:

0.282

Gnomad4 OTH exome

AF:

0.284

GnomAD4 genome

AF:

0.261

AC:

39642

AN:

152156

Hom.:

5937

Cov.:

AF XY:

0.267

AC XY:

19900

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.149

Gnomad4 AMR

AF:

0.418

Gnomad4 ASJ

AF:

0.192

Gnomad4 EAS

AF:

0.412

Gnomad4 SAS

AF:

0.358

Gnomad4 FIN

AF:

0.315

Gnomad4 NFE

AF:

0.269

Gnomad4 OTH

AF:

0.275

Alfa

AF:

0.263

Hom.:

5927

Bravo

AF:

0.263

Asia WGS

AF:

0.431

AC:

1497

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 17293876, 23052945) -

Exostoses, multiple, type 2

Benign:1

Jan 06, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

-0.88

CADD

Benign

7.6

DANN

Benign

0.84

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