rs1554820012
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The ENST00000320301.11(PCDH15):βc.5280_5342delβ(p.Ala1761_Pro1781del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000206 in 1,572,742 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (β β ). Synonymous variant affecting the same amino acid position (i.e. P1760P) has been classified as Likely benign.
Frequency
Consequence
ENST00000320301.11 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDH15 | NM_033056.4 | c.5280_5342del | p.Ala1761_Pro1781del | inframe_deletion | 33/33 | ENST00000320301.11 | NP_149045.3 | |
PCDH15 | NM_001384140.1 | c.4368-2216_4368-2154del | intron_variant | ENST00000644397.2 | NP_001371069.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000320301.11 | c.5280_5342del | p.Ala1761_Pro1781del | inframe_deletion | 33/33 | 1 | NM_033056.4 | ENSP00000322604 | ||
PCDH15 | ENST00000644397.2 | c.4368-2216_4368-2154del | intron_variant | NM_001384140.1 | ENSP00000495195 |
Frequencies
GnomAD3 genomes AF: 0.00121 AC: 183AN: 151128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000319 AC: 58AN: 182056Hom.: 0 AF XY: 0.000225 AC XY: 22AN XY: 97826
GnomAD4 exome AF: 0.0000992 AC: 141AN: 1421496Hom.: 0 AF XY: 0.0000895 AC XY: 63AN XY: 703916
GnomAD4 genome AF: 0.00121 AC: 183AN: 151246Hom.: 0 Cov.: 32 AF XY: 0.00104 AC XY: 77AN XY: 73868
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 27, 2022 | See Variant Classification Assertion Criteria. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 28, 2014 | Ala1761_Pro1781del in exon 33 of PCDH15: This variant is not expected to have cl inical significance because it has been identified in 0.8% (66/8214) of European American chromosomes and in 0.9% (39/4326) of African American chromosomes by t he NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/). In addit ion, the exon 33 region of PCDH15 is not conserved across species. - |
PCDH15-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 19, 2023 | 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). - |
Usher syndrome type 1F Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Feb 22, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at