chr2-86542289-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016079.4(CHMP3):c.69A>G(p.Ile23Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,613,492 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016079.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHMP3 | NM_016079.4 | c.69A>G | p.Ile23Met | missense_variant | 2/6 | ENST00000263856.9 | |
RNF103-CHMP3 | NM_001198954.1 | c.156A>G | p.Ile52Met | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHMP3 | ENST00000263856.9 | c.69A>G | p.Ile23Met | missense_variant | 2/6 | 1 | NM_016079.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251250Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135822
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461288Hom.: 1 Cov.: 30 AF XY: 0.0000316 AC XY: 23AN XY: 726950
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.69A>G (p.I23M) alteration is located in exon 2 (coding exon 2) of the CHMP3 gene. This alteration results from a A to G substitution at nucleotide position 69, causing the isoleucine (I) at amino acid position 23 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at