chr20-35627365-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152925.3(CPNE1):c.1151G>A(p.Arg384His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000737 in 1,614,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R384C) has been classified as Uncertain significance.
Frequency
Consequence
NM_152925.3 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 |
---|---|---|---|---|---|---|---|
CPNE1 | NM_152925.3 | c.1151G>A | p.Arg384His | missense_variant | 14/16 | ENST00000397443.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPNE1 | ENST00000397443.7 | c.1151G>A | p.Arg384His | missense_variant | 14/16 | 5 | NM_152925.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000441 AC: 67AN: 152084Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251442Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135888
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461862Hom.: 0 Cov.: 33 AF XY: 0.0000234 AC XY: 17AN XY: 727230
GnomAD4 genome AF: 0.000440 AC: 67AN: 152202Hom.: 0 Cov.: 31 AF XY: 0.000376 AC XY: 28AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 22, 2021 | The c.1166G>A (p.R389H) alteration is located in exon 14 (coding exon 14) of the CPNE1 gene. This alteration results from a G to A substitution at nucleotide position 1166, causing the arginine (R) at amino acid position 389 to be replaced by a histidine (H). 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