10-123757242-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_198148.3(CPXM2):c.1888C>T(p.Arg630Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000657 in 1,613,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPXM2 | NM_198148.3 | c.1888C>T | p.Arg630Trp | missense_variant | Exon 12 of 14 | ENST00000241305.4 | NP_937791.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPXM2 | ENST00000241305.4 | c.1888C>T | p.Arg630Trp | missense_variant | Exon 12 of 14 | 1 | NM_198148.3 | ENSP00000241305.3 | ||
CPXM2 | ENST00000615851.4 | c.376C>T | p.Arg126Trp | missense_variant | Exon 12 of 15 | 5 | ENSP00000483180.1 | |||
CPXM2 | ENST00000368854.7 | n.1935C>T | non_coding_transcript_exon_variant | Exon 14 of 20 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152130Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251472Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135906
GnomAD4 exome AF: 0.0000691 AC: 101AN: 1461778Hom.: 0 Cov.: 30 AF XY: 0.0000935 AC XY: 68AN XY: 727198
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152130Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1888C>T (p.R630W) alteration is located in exon 12 (coding exon 12) of the CPXM2 gene. This alteration results from a C to T substitution at nucleotide position 1888, causing the arginine (R) at amino acid position 630 to be replaced by a tryptophan (W). 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