rs74609306
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001384140.1(PCDH15):c.5124G>A(p.Lys1708Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.028 in 1,613,826 control chromosomes in the GnomAD database, including 740 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001384140.1 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.5124G>A | p.Lys1708Lys | synonymous_variant | Exon 38 of 38 | ENST00000644397.2 | NP_001371069.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000644397.2 | c.5124G>A | p.Lys1708Lys | synonymous_variant | Exon 38 of 38 | NM_001384140.1 | ENSP00000495195.1 |
Frequencies
GnomAD3 genomes AF: 0.0196 AC: 2976AN: 152112Hom.: 36 Cov.: 32
GnomAD3 exomes AF: 0.0192 AC: 4769AN: 248706Hom.: 68 AF XY: 0.0190 AC XY: 2562AN XY: 135132
GnomAD4 exome AF: 0.0289 AC: 42201AN: 1461596Hom.: 704 Cov.: 33 AF XY: 0.0281 AC XY: 20463AN XY: 727086
GnomAD4 genome AF: 0.0196 AC: 2978AN: 152230Hom.: 36 Cov.: 32 AF XY: 0.0184 AC XY: 1370AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:3
- -
- -
- -
not specified Benign:1
Lys1650Lys in Exon 37 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 2.8% (154/5446) of European American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs74609306). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at