chr3-194341955-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080513.4(CPN2):c.748C>T(p.Arg250Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000806 in 1,613,766 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_001080513.4 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 |
---|---|---|---|---|---|---|---|
CPN2 | NM_001080513.4 | c.748C>T | p.Arg250Cys | missense_variant | 2/2 | ENST00000323830.4 | |
CPN2 | NM_001291988.2 | c.748C>T | p.Arg250Cys | missense_variant | 2/2 | ||
CPN2 | XM_005269280.5 | c.748C>T | p.Arg250Cys | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPN2 | ENST00000323830.4 | c.748C>T | p.Arg250Cys | missense_variant | 2/2 | 1 | NM_001080513.4 | P1 | |
CPN2 | ENST00000429275.1 | c.748C>T | p.Arg250Cys | missense_variant | 2/2 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000176 AC: 44AN: 250326Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135558
GnomAD4 exome AF: 0.0000807 AC: 118AN: 1461568Hom.: 0 Cov.: 80 AF XY: 0.0000701 AC XY: 51AN XY: 727126
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 17, 2023 | The c.748C>T (p.R250C) alteration is located in exon 2 (coding exon 1) of the CPN2 gene. This alteration results from a C to T substitution at nucleotide position 748, causing the arginine (R) at amino acid position 250 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