chr5-140802063-T-C
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_018906.3(PCDHA3):c.866T>C(p.Ile289Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 1,614,098 control chromosomes in the GnomAD database, including 12,557 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_018906.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHA3 | NM_018906.3 | c.866T>C | p.Ile289Thr | missense_variant | Exon 1 of 4 | ENST00000522353.3 | NP_061729.1 | |
PCDHA1 | NM_018900.4 | c.2394+13379T>C | intron_variant | Intron 1 of 3 | ENST00000504120.4 | NP_061723.1 | ||
PCDHA2 | NM_018905.3 | c.2388+4711T>C | 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.866T>C | p.Ile289Thr | missense_variant | Exon 1 of 4 | 1 | NM_018906.3 | ENSP00000429808.2 | ||
PCDHA1 | ENST00000504120.4 | c.2394+13379T>C | intron_variant | Intron 1 of 3 | 1 | NM_018900.4 | ENSP00000420840.3 | |||
PCDHA2 | ENST00000526136.2 | c.2388+4711T>C | intron_variant | Intron 1 of 3 | 1 | NM_018905.3 | ENSP00000431748.1 |
Frequencies
GnomAD3 genomes AF: 0.108 AC: 16370AN: 152130Hom.: 1015 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.107 AC: 26793AN: 251414 AF XY: 0.107 show subpopulations
GnomAD4 exome AF: 0.121 AC: 177385AN: 1461850Hom.: 11542 Cov.: 88 AF XY: 0.120 AC XY: 87424AN XY: 727218 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.107 AC: 16361AN: 152248Hom.: 1015 Cov.: 33 AF XY: 0.110 AC XY: 8168AN XY: 74440 show subpopulations
Age Distribution
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