10-123761881-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198148.3(CPXM2):c.1768G>A(p.Val590Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000521 in 1,613,164 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198148.3 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 |
---|---|---|---|---|---|---|---|---|
CPXM2 | NM_198148.3 | c.1768G>A | p.Val590Ile | missense_variant | Exon 11 of 14 | ENST00000241305.4 | NP_937791.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPXM2 | ENST00000241305.4 | c.1768G>A | p.Val590Ile | missense_variant | Exon 11 of 14 | 1 | NM_198148.3 | ENSP00000241305.3 | ||
CPXM2 | ENST00000615851.4 | c.256G>A | p.Val86Ile | missense_variant | Exon 11 of 15 | 5 | ENSP00000483180.1 | |||
CPXM2 | ENST00000368854.7 | n.1815G>A | non_coding_transcript_exon_variant | Exon 13 of 20 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248298Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134368
GnomAD4 exome AF: 0.0000541 AC: 79AN: 1460976Hom.: 1 Cov.: 31 AF XY: 0.0000660 AC XY: 48AN XY: 726756
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1768G>A (p.V590I) alteration is located in exon 11 (coding exon 11) of the CPXM2 gene. This alteration results from a G to A substitution at nucleotide position 1768, causing the valine (V) at amino acid position 590 to be replaced by an isoleucine (I). 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