chr3-194341097-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080513.4(CPN2):c.1606G>A(p.Val536Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 1,607,610 control chromosomes in the GnomAD database, including 66,914 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001080513.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPN2 | NM_001080513.4 | c.1606G>A | p.Val536Met | missense_variant | 2/2 | ENST00000323830.4 | |
CPN2 | NM_001291988.2 | c.1606G>A | p.Val536Met | missense_variant | 2/2 | ||
CPN2 | XM_005269280.5 | c.1606G>A | p.Val536Met | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPN2 | ENST00000323830.4 | c.1606G>A | p.Val536Met | missense_variant | 2/2 | 1 | NM_001080513.4 | P1 | |
CPN2 | ENST00000429275.1 | c.1606G>A | p.Val536Met | missense_variant | 2/2 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.260 AC: 39503AN: 152070Hom.: 5401 Cov.: 33
GnomAD3 exomes AF: 0.289 AC: 71781AN: 248410Hom.: 11056 AF XY: 0.297 AC XY: 39974AN XY: 134492
GnomAD4 exome AF: 0.287 AC: 417851AN: 1455422Hom.: 61515 Cov.: 34 AF XY: 0.291 AC XY: 210203AN XY: 722926
GnomAD4 genome ? AF: 0.260 AC: 39505AN: 152188Hom.: 5399 Cov.: 33 AF XY: 0.265 AC XY: 19729AN XY: 74416
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at