10-53808767-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001142769.3(PCDH15):c.5298G>A(p.Ala1766Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00787 in 1,612,442 control chromosomes in the GnomAD database, including 58 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001142769.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDH15 | NM_001384140.1 | c.4672-1637G>A | intron_variant | Intron 37 of 37 | ENST00000644397.2 | NP_001371069.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000644397.2 | c.4672-1637G>A | intron_variant | Intron 37 of 37 | NM_001384140.1 | ENSP00000495195.1 |
Frequencies
GnomAD3 genomes AF: 0.00702 AC: 1067AN: 152082Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00699 AC: 1718AN: 245870Hom.: 13 AF XY: 0.00693 AC XY: 926AN XY: 133562
GnomAD4 exome AF: 0.00796 AC: 11629AN: 1460242Hom.: 52 Cov.: 31 AF XY: 0.00776 AC XY: 5636AN XY: 726220
GnomAD4 genome AF: 0.00702 AC: 1068AN: 152200Hom.: 6 Cov.: 32 AF XY: 0.00764 AC XY: 568AN XY: 74390
ClinVar
Submissions by phenotype
not provided Benign:5
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PCDH15: BP4, BP7, BS2 -
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not specified Benign:2
Ala1766Ala in Exon 37A of PCDH15: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wit hin the splice consensus sequence, and has been identified in 0.7% (40/5446) of European American chromosomes from a broad population by the NHLBI Exome Sequenc ing Project (http://evs.gs.washington.edu/EVS; dbSNP rs139441645). -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at