rs188859975
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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
NM_000127.3 missense
Scores
6
13
Clinical Significance
Conservation
PhyloP100: 5.21
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]
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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 |
---|---|---|---|---|---|---|---|---|
EXT1 | NM_000127.3 | c.1457C>T | p.Ala486Val | missense_variant | 6/11 | ENST00000378204.7 | NP_000118.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EXT1 | ENST00000378204.7 | c.1457C>T | p.Ala486Val | missense_variant | 6/11 | 1 | NM_000127.3 | ENSP00000367446.3 | ||
EXT1 | ENST00000437196.1 | n.*348C>T | non_coding_transcript_exon_variant | 5/10 | 5 | ENSP00000407299.1 | ||||
EXT1 | ENST00000684189.1 | n.924C>T | non_coding_transcript_exon_variant | 6/11 | ||||||
EXT1 | ENST00000437196.1 | n.*348C>T | 3_prime_UTR_variant | 5/10 | 5 | ENSP00000407299.1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152166Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000247 AC: 62AN: 251190Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135748
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GnomAD4 exome AF: 0.000107 AC: 156AN: 1461128Hom.: 1 Cov.: 31 AF XY: 0.000111 AC XY: 81AN XY: 726852
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GnomAD4 genome AF: 0.000118 AC: 18AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74470
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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 provided | research | Department of Pediatrics, Samsung Medical Center, Samsung Medical Center | - | - - |
Multiple congenital exostosis Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | - - |
EXT1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 01, 2019 | This 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 provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Benign
DEOGEN2
Uncertain
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at