3-87240720-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_014043.4(CHMP2B):c.56G>A(p.Arg19Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000911 in 1,613,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_014043.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHMP2B | NM_014043.4 | c.56G>A | p.Arg19Gln | missense_variant | Exon 2 of 6 | ENST00000263780.9 | NP_054762.2 | |
CHMP2B | NM_001410777.1 | c.152G>A | p.Arg51Gln | missense_variant | Exon 3 of 7 | NP_001397706.1 | ||
CHMP2B | XM_011533576.3 | c.104G>A | p.Arg35Gln | missense_variant | Exon 2 of 6 | XP_011531878.1 | ||
CHMP2B | NM_001244644.2 | c.4-4994G>A | intron_variant | Intron 1 of 4 | NP_001231573.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251184Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135750
GnomAD4 exome AF: 0.0000931 AC: 136AN: 1460786Hom.: 0 Cov.: 29 AF XY: 0.0000977 AC XY: 71AN XY: 726810
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74428
ClinVar
Submissions by phenotype
Frontotemporal dementia and/or amyotrophic lateral sclerosis 7 Uncertain:2Benign:1
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 19 of the CHMP2B protein (p.Arg19Gln). This variant is present in population databases (rs200322526, gnomAD 0.02%). This missense change has been observed in individual(s) with parkinsonism-dementia complex (PMID: 25558820). ClinVar contains an entry for this variant (Variation ID: 902088). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
CHMP2B-related disorder Uncertain:1
The CHMP2B c.56G>A variant is predicted to result in the amino acid substitution p.Arg19Gln. This variant was reported in an individual with parkinsonism-dementia complex but was also observed in two unaffected controls age 57 and 71 (Steele et al 2015. PubMed ID: 25558820). This variant is reported in 0.020% of alleles in individuals of East Asian descent in gnomAD. This variant could be benign. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at