3-194341559-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080513.4(CPN2):c.1144G>A(p.Asp382Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,944 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_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.1144G>A | p.Asp382Asn | missense_variant | 2/2 | ENST00000323830.4 | |
CPN2 | NM_001291988.2 | c.1144G>A | p.Asp382Asn | missense_variant | 2/2 | ||
CPN2 | XM_005269280.5 | c.1144G>A | p.Asp382Asn | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPN2 | ENST00000323830.4 | c.1144G>A | p.Asp382Asn | missense_variant | 2/2 | 1 | NM_001080513.4 | P1 | |
CPN2 | ENST00000429275.1 | c.1144G>A | p.Asp382Asn | missense_variant | 2/2 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152086Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251436Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135908
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461858Hom.: 0 Cov.: 86 AF XY: 0.00000550 AC XY: 4AN XY: 727238
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152086Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.1144G>A (p.D382N) alteration is located in exon 2 (coding exon 1) of the CPN2 gene. This alteration results from a G to A substitution at nucleotide position 1144, causing the aspartic acid (D) at amino acid position 382 to be replaced by an asparagine (N). 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