10-123757305-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198148.3(CPXM2):c.1825A>G(p.Ile609Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000868 in 1,613,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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.1825A>G | p.Ile609Val | 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.1825A>G | p.Ile609Val | missense_variant | Exon 12 of 14 | 1 | NM_198148.3 | ENSP00000241305.3 | ||
CPXM2 | ENST00000615851.4 | c.313A>G | p.Ile105Val | missense_variant | Exon 12 of 15 | 5 | ENSP00000483180.1 | |||
CPXM2 | ENST00000368854.7 | n.1872A>G | non_coding_transcript_exon_variant | Exon 14 of 20 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251478Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135912
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461518Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 727100
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1825A>G (p.I609V) alteration is located in exon 12 (coding exon 12) of the CPXM2 gene. This alteration results from a A to G substitution at nucleotide position 1825, causing the isoleucine (I) at amino acid position 609 to be replaced by a valine (V). 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