NM_005026.5:c.4C>A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_005026.5(PIK3CD):c.4C>A(p.Pro2Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000874 in 1,613,946 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P2L) has been classified as Uncertain significance.
Frequency
Consequence
NM_005026.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIK3CD | NM_005026.5 | c.4C>A | p.Pro2Thr | missense_variant | Exon 3 of 24 | ENST00000377346.9 | NP_005017.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152132Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251446Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135904
GnomAD4 exome AF: 0.0000937 AC: 137AN: 1461696Hom.: 0 Cov.: 31 AF XY: 0.000127 AC XY: 92AN XY: 727174
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152250Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74426
ClinVar
Submissions by phenotype
Immunodeficiency 14 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at