chr12-68856535-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198320.5(CPM):c.1234A>G(p.Met412Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,614,256 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198320.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPM | NM_198320.5 | c.1234A>G | p.Met412Val | missense_variant | 9/9 | ENST00000551568.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPM | ENST00000551568.6 | c.1234A>G | p.Met412Val | missense_variant | 9/9 | 1 | NM_198320.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000722 AC: 11AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251394Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135860
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727246
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.1234A>G (p.M412V) alteration is located in exon 9 (coding exon 8) of the CPM gene. This alteration results from a A to G substitution at nucleotide position 1234, causing the methionine (M) at amino acid position 412 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