20-35627366-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_152925.3(CPNE1):c.1150C>T(p.Arg384Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,614,050 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. R384H) 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPNE1 | NM_152925.3 | c.1150C>T | p.Arg384Cys | missense_variant | 14/16 | ENST00000397443.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPNE1 | ENST00000397443.7 | c.1150C>T | p.Arg384Cys | missense_variant | 14/16 | 5 | NM_152925.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152074Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251440Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135896
GnomAD4 exome AF: 0.000174 AC: 255AN: 1461858Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 127AN XY: 727234
GnomAD4 genome AF: 0.000125 AC: 19AN: 152192Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.1165C>T (p.R389C) alteration is located in exon 14 (coding exon 14) of the CPNE1 gene. This alteration results from a C to T substitution at nucleotide position 1165, causing the arginine (R) at amino acid position 389 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