11-44231853-G-C

Position:

• chr11-44231853-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_207122.2(EXT2):​c.1663-500G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,052 control chromosomes in the GnomAD database, including 5,567 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (5567 hom., cov: 32)
• Consequence: EXT2 NM_207122.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.507

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 11-44231853-G-C is Benign according to our data. Variant chr11-44231853-G-C is described in ClinVar as [Benign]. Clinvar id is 263288.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EXT2	NM_207122.2	c.1663-500G>C		intron_variant		ENST00000533608.7	NP_997005.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EXT2	ENST00000533608.7	c.1663-500G>C		intron_variant		1	NM_207122.2	ENSP00000431173.2

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36985 AN: 151934 Hom.: 5550 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.259

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.243 AC: 37019 AN: 152052 Hom.: 5567 Cov.: 32 AF XY: 0.251 AC XY: 18644 AN XY: 74314

Gnomad4 AFR AF: 0.0924

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.267

Alfa AF: 0.247 Hom.: 749

Bravo AF: 0.244

Asia WGS AF: 0.419 AC: 1456 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.31
DANN	Benign	0.41

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

Other links and lift over

dbSNP: rs1113132; hg19: chr11-44253403;