rs76901081
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP3BP4_StrongBS1BS2
The NM_207122.2(EXT2):c.896G>A(p.Arg299His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00025 in 1,613,646 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R299C) has been classified as Uncertain significance.
Frequency
Consequence
NM_207122.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXT2 | NM_207122.2 | c.896G>A | p.Arg299His | missense_variant | 5/14 | ENST00000533608.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXT2 | ENST00000533608.7 | c.896G>A | p.Arg299His | missense_variant | 5/14 | 1 | NM_207122.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000565 AC: 142AN: 251222Hom.: 0 AF XY: 0.000508 AC XY: 69AN XY: 135776
GnomAD4 exome AF: 0.000253 AC: 369AN: 1461384Hom.: 3 Cov.: 32 AF XY: 0.000243 AC XY: 177AN XY: 727014
GnomAD4 genome AF: 0.000230 AC: 35AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74452
ClinVar
Submissions by phenotype
Exostoses, multiple, type 2 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at