12-68866971-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198320.5(CPM):c.865C>T(p.Arg289Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,006 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R289G) has been classified as Uncertain significance.
Frequency
Consequence
NM_198320.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPM | NM_198320.5 | c.865C>T | p.Arg289Cys | missense_variant | 7/9 | ENST00000551568.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPM | ENST00000551568.6 | c.865C>T | p.Arg289Cys | missense_variant | 7/9 | 1 | NM_198320.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251288Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135810
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461738Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727184
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 17, 2023 | The c.865C>T (p.R289C) alteration is located in exon 7 (coding exon 6) of the CPM gene. This alteration results from a C to T substitution at nucleotide position 865, causing the arginine (R) at amino acid position 289 to be replaced by a cysteine (C). 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