8-86554947-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003909.5(CPNE3):c.1217G>A(p.Arg406Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003909.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPNE3 | NM_003909.5 | c.1217G>A | p.Arg406Lys | missense_variant | 15/17 | ENST00000517490.6 | NP_003900.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPNE3 | ENST00000517490.6 | c.1217G>A | p.Arg406Lys | missense_variant | 15/17 | 1 | NM_003909.5 | ENSP00000477590 | P1 | |
CPNE3 | ENST00000614678.1 | n.803G>A | non_coding_transcript_exon_variant | 5/7 | 1 | |||||
CNGB3 | ENST00000517327.5 | c.*15-821C>T | intron_variant | 3 | ENSP00000428329 | |||||
CPNE3 | ENST00000517354.5 | n.534G>A | non_coding_transcript_exon_variant | 5/5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251462Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135908
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461842Hom.: 0 Cov.: 33 AF XY: 0.0000275 AC XY: 20AN XY: 727224
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.1217G>A (p.R406K) alteration is located in exon 15 (coding exon 13) of the CPNE3 gene. This alteration results from a G to A substitution at nucleotide position 1217, causing the arginine (R) at amino acid position 406 to be replaced by a lysine (K). 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