19-18211054-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001098818.4(PDE4C):c.1918G>A(p.Glu640Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,614,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001098818.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDE4C | ENST00000262805.17 | c.1918G>A | p.Glu640Lys | missense_variant | Exon 15 of 15 | 1 | NM_001098818.4 | ENSP00000262805.10 | ||
ENSG00000285188 | ENST00000355502.7 | c.2014G>A | p.Glu672Lys | missense_variant | Exon 19 of 19 | 2 | ENSP00000347689.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250968Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135672
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 727242
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2014G>A (p.E672K) alteration is located in exon 16 (coding exon 15) of the PDE4C gene. This alteration results from a G to A substitution at nucleotide position 2014, causing the glutamic acid (E) at amino acid position 672 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