20-35627306-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152925.3(CPNE1):āc.1210C>Gā(p.Gln404Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 1,611,756 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 (ā ).
Frequency
Consequence
NM_152925.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPNE1 | NM_152925.3 | c.1210C>G | p.Gln404Glu | missense_variant | 14/16 | ENST00000397443.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPNE1 | ENST00000397443.7 | c.1210C>G | p.Gln404Glu | missense_variant | 14/16 | 5 | NM_152925.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000173 AC: 26AN: 149948Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000725 AC: 18AN: 248188Hom.: 0 AF XY: 0.0000597 AC XY: 8AN XY: 133992
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461692Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 727152
GnomAD4 genome AF: 0.000173 AC: 26AN: 150064Hom.: 0 Cov.: 30 AF XY: 0.000218 AC XY: 16AN XY: 73322
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at