rs61730634
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_018906.3(PCDHA3):āc.411A>Gā(p.Val137Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0213 in 1,614,172 control chromosomes in the GnomAD database, including 441 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_018906.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHA3 | NM_018906.3 | c.411A>G | p.Val137Val | synonymous_variant | Exon 1 of 4 | ENST00000522353.3 | NP_061729.1 | |
PCDHA1 | NM_018900.4 | c.2394+12924A>G | intron_variant | Intron 1 of 3 | ENST00000504120.4 | NP_061723.1 | ||
PCDHA2 | NM_018905.3 | c.2388+4256A>G | 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.411A>G | p.Val137Val | synonymous_variant | Exon 1 of 4 | 1 | NM_018906.3 | ENSP00000429808.2 | ||
PCDHA1 | ENST00000504120.4 | c.2394+12924A>G | intron_variant | Intron 1 of 3 | 1 | NM_018900.4 | ENSP00000420840.3 | |||
PCDHA2 | ENST00000526136.2 | c.2388+4256A>G | intron_variant | Intron 1 of 3 | 1 | NM_018905.3 | ENSP00000431748.1 |
Frequencies
GnomAD3 genomes AF: 0.0151 AC: 2296AN: 152160Hom.: 38 Cov.: 33
GnomAD3 exomes AF: 0.0148 AC: 3721AN: 251468Hom.: 48 AF XY: 0.0148 AC XY: 2008AN XY: 135910
GnomAD4 exome AF: 0.0219 AC: 32083AN: 1461894Hom.: 403 Cov.: 92 AF XY: 0.0212 AC XY: 15416AN XY: 727248
GnomAD4 genome AF: 0.0151 AC: 2296AN: 152278Hom.: 38 Cov.: 33 AF XY: 0.0149 AC XY: 1108AN XY: 74468
ClinVar
Submissions by phenotype
PCDHA3-related disorder Benign:1
This variant is classified as 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