rs188859975

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_000127.3(EXT1):​c.1457C>T​(p.Ala486Val) variant causes a missense change. The variant allele was found at a frequency of 0.000108 in 1,613,412 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 1 hom. )

Consequence

EXT1
NM_000127.3 missense

Scores

6
13

Clinical Significance

Benign criteria provided, single submitter U:1B:2O:1

Conservation

PhyloP100: 5.21
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 (MetaRNN=0.019926697).
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000118 (18/152284) while in subpopulation EAS AF= 0.0029 (15/5176). AF 95% confidence interval is 0.00179. There are 0 homozygotes in gnomad4. There are 7 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 18 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EXT1NM_000127.3 linkuse as main transcriptc.1457C>T p.Ala486Val missense_variant 6/11 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.1457C>T p.Ala486Val missense_variant 6/111 NM_000127.3 ENSP00000367446.3 Q16394
EXT1ENST00000437196.1 linkuse as main transcriptn.*348C>T non_coding_transcript_exon_variant 5/105 ENSP00000407299.1 F8WF54
EXT1ENST00000684189.1 linkuse as main transcriptn.924C>T non_coding_transcript_exon_variant 6/11
EXT1ENST00000437196.1 linkuse as main transcriptn.*348C>T 3_prime_UTR_variant 5/105 ENSP00000407299.1 F8WF54

Frequencies

GnomAD3 genomes
AF:
0.000125
AC:
19
AN:
152166
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00308
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000247
AC:
62
AN:
251190
Hom.:
0
AF XY:
0.000236
AC XY:
32
AN XY:
135748
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00299
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000176
Gnomad OTH exome
AF:
0.000327
GnomAD4 exome
AF:
0.000107
AC:
156
AN:
1461128
Hom.:
1
Cov.:
31
AF XY:
0.000111
AC XY:
81
AN XY:
726852
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000447
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00353
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000360
Gnomad4 OTH exome
AF:
0.0000829
GnomAD4 genome
AF:
0.000118
AC:
18
AN:
152284
Hom.:
0
Cov.:
32
AF XY:
0.0000940
AC XY:
7
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00290
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000186
Hom.:
0
Bravo
AF:
0.000132
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.000231
AC:
28

ClinVar

Significance: Benign
Submissions summary: Uncertain:1Benign:2Other:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Microcephaly Uncertain:1
Uncertain significance, no assertion criteria providedresearchDepartment of Pediatrics, Samsung Medical Center, Samsung Medical Center-- -
Multiple congenital exostosis Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 24, 2024- -
EXT1-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesOct 01, 2019This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not specified Other:1
not provided, no classification providedreference populationITMISep 19, 2013- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.090
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Uncertain
0.050
CADD
Uncertain
23
DANN
Benign
0.45
DEOGEN2
Uncertain
0.46
T
Eigen
Benign
-0.073
Eigen_PC
Benign
0.18
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Uncertain
0.94
D
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.020
T
MetaSVM
Benign
-0.59
T
MutationAssessor
Benign
0.59
N
PrimateAI
Uncertain
0.73
T
PROVEAN
Benign
0.050
N
REVEL
Uncertain
0.38
Sift
Benign
1.0
T
Sift4G
Benign
1.0
T
Polyphen
0.014
B
Vest4
0.69
MVP
0.85
MPC
0.41
ClinPred
0.031
T
GERP RS
5.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.6
Varity_R
0.17
gMVP
0.75

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: rs188859975; hg19: chr8-118831994; COSMIC: COSV65479378; API