5-140801491-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_018906.3(PCDHA3):c.294G>A(p.Arg98Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 1,614,176 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_018906.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHA3 | NM_018906.3 | c.294G>A | p.Arg98Arg | synonymous_variant | Exon 1 of 4 | ENST00000522353.3 | NP_061729.1 | |
PCDHA1 | NM_018900.4 | c.2394+12807G>A | intron_variant | Intron 1 of 3 | ENST00000504120.4 | NP_061723.1 | ||
PCDHA2 | NM_018905.3 | c.2388+4139G>A | 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.294G>A | p.Arg98Arg | synonymous_variant | Exon 1 of 4 | 1 | NM_018906.3 | ENSP00000429808.2 | ||
PCDHA1 | ENST00000504120.4 | c.2394+12807G>A | intron_variant | Intron 1 of 3 | 1 | NM_018900.4 | ENSP00000420840.3 | |||
PCDHA2 | ENST00000526136.2 | c.2388+4139G>A | intron_variant | Intron 1 of 3 | 1 | NM_018905.3 | ENSP00000431748.1 |
Frequencies
GnomAD3 genomes AF: 0.000795 AC: 121AN: 152282Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000573 AC: 144AN: 251484Hom.: 0 AF XY: 0.000640 AC XY: 87AN XY: 135920
GnomAD4 exome AF: 0.00118 AC: 1724AN: 1461776Hom.: 3 Cov.: 92 AF XY: 0.00112 AC XY: 814AN XY: 727190
GnomAD4 genome AF: 0.000794 AC: 121AN: 152400Hom.: 0 Cov.: 33 AF XY: 0.000899 AC XY: 67AN XY: 74526
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