chr19-58551759-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014453.4(CHMP2A):c.559G>A(p.Gly187Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G187R) has been classified as Uncertain significance.
Frequency
Consequence
NM_014453.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHMP2A | NM_014453.4 | c.559G>A | p.Gly187Ser | missense_variant | Exon 6 of 6 | ENST00000312547.7 | NP_055268.1 | |
CHMP2A | NM_198426.3 | c.559G>A | p.Gly187Ser | missense_variant | Exon 6 of 6 | NP_940818.1 | ||
CHMP2A | XM_005258746.3 | c.688G>A | p.Gly230Ser | missense_variant | Exon 5 of 5 | XP_005258803.1 | ||
CHMP2A | XM_005258747.4 | c.688G>A | p.Gly230Ser | missense_variant | Exon 5 of 5 | XP_005258804.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727226
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at