NM_018906.3:c.526_529delGAAT
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_018906.3(PCDHA3):c.526_529delGAAT(p.Glu176IlefsTer20) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 1,614,106 control chromosomes in the GnomAD database, including 133 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_018906.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHA3 | NM_018906.3 | c.526_529delGAAT | p.Glu176IlefsTer20 | frameshift_variant | Exon 1 of 4 | ENST00000522353.3 | NP_061729.1 | |
PCDHA1 | NM_018900.4 | c.2394+13039_2394+13042delGAAT | intron_variant | Intron 1 of 3 | ENST00000504120.4 | NP_061723.1 | ||
PCDHA2 | NM_018905.3 | c.2388+4371_2388+4374delGAAT | intron_variant | Intron 1 of 3 | ENST00000526136.2 | NP_061728.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHA3 | ENST00000522353.3 | c.526_529delGAAT | p.Glu176IlefsTer20 | frameshift_variant | Exon 1 of 4 | 1 | NM_018906.3 | ENSP00000429808.2 | ||
PCDHA1 | ENST00000504120.4 | c.2394+13039_2394+13042delGAAT | intron_variant | Intron 1 of 3 | 1 | NM_018900.4 | ENSP00000420840.3 | |||
PCDHA2 | ENST00000526136.2 | c.2388+4371_2388+4374delGAAT | intron_variant | Intron 1 of 3 | 1 | NM_018905.3 | ENSP00000431748.1 |
Frequencies
GnomAD3 genomes AF: 0.00960 AC: 1461AN: 152134Hom.: 11 Cov.: 33
GnomAD3 exomes AF: 0.00963 AC: 2421AN: 251358Hom.: 28 AF XY: 0.00972 AC XY: 1321AN XY: 135884
GnomAD4 exome AF: 0.0114 AC: 16698AN: 1461854Hom.: 122 AF XY: 0.0110 AC XY: 8001AN XY: 727220
GnomAD4 genome AF: 0.00960 AC: 1461AN: 152252Hom.: 11 Cov.: 33 AF XY: 0.0102 AC XY: 758AN XY: 74428
ClinVar
Submissions by phenotype
PCDHA3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at