rs11989122
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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
NM_000127.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.129
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 (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 |
---|---|---|---|---|---|---|---|---|
EXT1 | NM_000127.3 | c.1633-2639C>T | intron_variant | ENST00000378204.7 | NP_000118.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EXT1 | ENST00000378204.7 | c.1633-2639C>T | intron_variant | 1 | NM_000127.3 | ENSP00000367446.3 | ||||
EXT1 | ENST00000437196.1 | n.*524-2639C>T | intron_variant | 5 | ENSP00000407299.1 | |||||
EXT1 | ENST00000684189.1 | n.1100-2639C>T | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.672 AC: 102080AN: 151942Hom.: 34442 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.672 AC: 102176AN: 152060Hom.: 34480 Cov.: 32 AF XY: 0.669 AC XY: 49706AN XY: 74334
GnomAD4 genome
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2006
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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