10-123761901-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_198148.3(CPXM2):c.1748A>G(p.Asn583Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,613,684 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 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPXM2 | NM_198148.3 | c.1748A>G | p.Asn583Ser | 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.1748A>G | p.Asn583Ser | missense_variant | Exon 11 of 14 | 1 | NM_198148.3 | ENSP00000241305.3 | ||
CPXM2 | ENST00000615851.4 | c.236A>G | p.Asn79Ser | missense_variant | Exon 11 of 15 | 5 | ENSP00000483180.1 | |||
CPXM2 | ENST00000368854.7 | n.1795A>G | non_coding_transcript_exon_variant | Exon 13 of 20 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 249904Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135188
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461530Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727066
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1748A>G (p.N583S) alteration is located in exon 11 (coding exon 11) of the CPXM2 gene. This alteration results from a A to G substitution at nucleotide position 1748, causing the asparagine (N) at amino acid position 583 to be replaced by a serine (S). 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