rs11989122

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000127.3(EXT1):​c.1633-2639C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,060 control chromosomes in the GnomAD database, including 34,480 homozygotes. 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 0.67 ( 34480 hom., cov: 32)

Consequence

EXT1
NM_000127.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.129
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EXT1NM_000127.3 linkuse as main transcriptc.1633-2639C>T intron_variant ENST00000378204.7 NP_000118.2 Q16394

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EXT1ENST00000378204.7 linkuse as main transcriptc.1633-2639C>T intron_variant 1 NM_000127.3 ENSP00000367446.3 Q16394
EXT1ENST00000437196.1 linkuse as main transcriptn.*524-2639C>T intron_variant 5 ENSP00000407299.1 F8WF54
EXT1ENST00000684189.1 linkuse as main transcriptn.1100-2639C>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.672
AC:
102080
AN:
151942
Hom.:
34442
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.647
Gnomad AMI
AF:
0.547
Gnomad AMR
AF:
0.736
Gnomad ASJ
AF:
0.723
Gnomad EAS
AF:
0.575
Gnomad SAS
AF:
0.606
Gnomad FIN
AF:
0.661
Gnomad MID
AF:
0.694
Gnomad NFE
AF:
0.685
Gnomad OTH
AF:
0.691
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.672
AC:
102176
AN:
152060
Hom.:
34480
Cov.:
32
AF XY:
0.669
AC XY:
49706
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.647
Gnomad4 AMR
AF:
0.736
Gnomad4 ASJ
AF:
0.723
Gnomad4 EAS
AF:
0.575
Gnomad4 SAS
AF:
0.605
Gnomad4 FIN
AF:
0.661
Gnomad4 NFE
AF:
0.685
Gnomad4 OTH
AF:
0.694
Alfa
AF:
0.687
Hom.:
65279
Bravo
AF:
0.678
Asia WGS
AF:
0.577
AC:
2006
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
10
DANN
Benign
0.53

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.

Other links and lift over

dbSNP: rs11989122; hg19: chr8-118827839; API