chr5-173890203-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_030627.4(CPEB4):c.470C>A(p.Pro157His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000785 in 1,614,054 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 (★).
Frequency
Consequence
NM_030627.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPEB4 | NM_030627.4 | c.470C>A | p.Pro157His | missense_variant | Exon 1 of 10 | ENST00000265085.10 | NP_085130.2 | |
CPEB4 | NM_001308189.2 | c.470C>A | p.Pro157His | missense_variant | Exon 1 of 9 | NP_001295118.1 | ||
CPEB4 | NM_001308191.2 | c.470C>A | p.Pro157His | missense_variant | Exon 1 of 8 | NP_001295120.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPEB4 | ENST00000265085.10 | c.470C>A | p.Pro157His | missense_variant | Exon 1 of 10 | 1 | NM_030627.4 | ENSP00000265085.5 | ||
CPEB4 | ENST00000334035.9 | c.470C>A | p.Pro157His | missense_variant | Exon 1 of 9 | 1 | ENSP00000334533.5 | |||
CPEB4 | ENST00000520867.5 | c.470C>A | p.Pro157His | missense_variant | Exon 1 of 8 | 1 | ENSP00000429092.1 | |||
CPEB4 | ENST00000519835.5 | c.470C>A | p.Pro157His | missense_variant | Exon 1 of 7 | 1 | ENSP00000429048.1 |
Frequencies
GnomAD3 genomes AF: 0.000486 AC: 74AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000541 AC: 136AN: 251222Hom.: 0 AF XY: 0.000552 AC XY: 75AN XY: 135830
GnomAD4 exome AF: 0.000816 AC: 1193AN: 1461846Hom.: 0 Cov.: 33 AF XY: 0.000737 AC XY: 536AN XY: 727220
GnomAD4 genome AF: 0.000486 AC: 74AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000417 AC XY: 31AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.470C>A (p.P157H) alteration is located in exon 1 (coding exon 1) of the CPEB4 gene. This alteration results from a C to A substitution at nucleotide position 470, causing the proline (P) at amino acid position 157 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