rs3740878
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_207122.2(EXT2):c.1936-41T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 1,580,138 control chromosomes in the GnomAD database, including 70,507 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.25 ( 5665 hom., cov: 32)
Exomes 𝑓: 0.29 ( 64842 hom. )
Consequence
EXT2
NM_207122.2 intron
NM_207122.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.481
Genes affected
EXT2 (HGNC:3513): (exostosin glycosyltransferase 2) This gene encodes one of two glycosyltransferases involved in the chain elongation step of heparan sulfate biosynthesis. Mutations in this gene cause the type II form of multiple exostoses. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 11-44236252-T-C is Benign according to our data. Variant chr11-44236252-T-C is described in ClinVar as [Benign]. Clinvar id is 263290.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXT2 | NM_207122.2 | c.1936-41T>C | intron_variant | ENST00000533608.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXT2 | ENST00000533608.7 | c.1936-41T>C | intron_variant | 1 | NM_207122.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.246 AC: 37388AN: 151972Hom.: 5648 Cov.: 32
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GnomAD3 exomes AF: 0.318 AC: 79304AN: 249662Hom.: 14531 AF XY: 0.315 AC XY: 42484AN XY: 134940
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GnomAD4 exome AF: 0.292 AC: 417325AN: 1428046Hom.: 64842 Cov.: 24 AF XY: 0.293 AC XY: 208986AN XY: 712592
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GnomAD4 genome ? AF: 0.246 AC: 37424AN: 152092Hom.: 5665 Cov.: 32 AF XY: 0.253 AC XY: 18838AN XY: 74338
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Exostoses, multiple, type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | This variant is associated with the following publications: (PMID: 17293876, 23052945) - |
Exostoses, multiple, type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Computational scores
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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