GeneBe

8-117866683-A-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000127.3(EXT1):​c.963-29482T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 28)
Failed GnomAD Quality Control

Consequence

EXT1
NM_000127.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0150

Publications

1 publications found
Variant links:
Genes affected
EXT1 (HGNC:3512): (exostosin glycosyltransferase 1) This gene encodes an endoplasmic reticulum-resident type II transmembrane glycosyltransferase involved in the chain elongation step of heparan sulfate biosynthesis. Mutations in this gene cause the type I form of multiple exostoses. [provided by RefSeq, Jul 2008]
EXT1 Gene-Disease associations (from GenCC):
  • exostoses, multiple, type 1
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen
  • chondrosarcoma
    Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
  • hereditary multiple osteochondromas
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EXT1NM_000127.3 linkc.963-29482T>A intron_variant Intron 1 of 10 ENST00000378204.7 NP_000118.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EXT1ENST00000378204.7 linkc.963-29482T>A intron_variant Intron 1 of 10 1 NM_000127.3 ENSP00000367446.3
EXT1ENST00000436216.2 linkn.330-29482T>A intron_variant Intron 1 of 5 3 ENSP00000400372.1
EXT1ENST00000437196.1 linkn.74-31132T>A intron_variant Intron 1 of 9 5 ENSP00000407299.1
EXT1ENST00000684189.1 linkn.430-29482T>A intron_variant Intron 1 of 10

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
151956
Hom.:
0
Cov.:
28
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
151956
Hom.:
0
Cov.:
28
AF XY:
0.00
AC XY:
0
AN XY:
74198
African (AFR)
AF:
0.00
AC:
0
AN:
41350
American (AMR)
AF:
0.00
AC:
0
AN:
15250
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5158
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4808
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10584
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
68020
Other (OTH)
AF:
0.00
AC:
0
AN:
2086
Alfa
AF:
0.00
Hom.:
10237

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
7.5
DANN
Benign
0.79
PhyloP100
0.015

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

Other links and lift over

dbSNP: rs6469713; hg19: chr8-118878922; API