19-58551708-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014453.4(CHMP2A):c.610G>A(p.Ala204Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,614,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHMP2A | NM_014453.4 | c.610G>A | p.Ala204Thr | missense_variant | Exon 6 of 6 | ENST00000312547.7 | NP_055268.1 | |
CHMP2A | NM_198426.3 | c.610G>A | p.Ala204Thr | missense_variant | Exon 6 of 6 | NP_940818.1 | ||
CHMP2A | XM_005258746.3 | c.739G>A | p.Ala247Thr | missense_variant | Exon 5 of 5 | XP_005258803.1 | ||
CHMP2A | XM_005258747.4 | c.739G>A | p.Ala247Thr | missense_variant | Exon 5 of 5 | XP_005258804.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251240Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135866
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461816Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 38AN XY: 727198
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.610G>A (p.A204T) alteration is located in exon 6 (coding exon 5) of the CHMP2A gene. This alteration results from a G to A substitution at nucleotide position 610, causing the alanine (A) at amino acid position 204 to be replaced by a threonine (T). 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