rs373916538
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_033056.4(PCDH15):βc.5278_5286delβ(p.Pro1760_Pro1762del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00022 in 1,587,340 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
NM_033056.4 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 | UniProt |
---|---|---|---|---|---|---|---|
PCDH15 | NM_033056.4 | c.5278_5286del | p.Pro1760_Pro1762del | inframe_deletion | 33/33 | ENST00000320301.11 | |
PCDH15 | NM_001384140.1 | c.4368-2218_4368-2210del | intron_variant | ENST00000644397.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000320301.11 | c.5278_5286del | p.Pro1760_Pro1762del | inframe_deletion | 33/33 | 1 | NM_033056.4 | ||
PCDH15 | ENST00000644397.2 | c.4368-2218_4368-2210del | intron_variant | NM_001384140.1 |
Frequencies
GnomAD3 genomes AF: 0.00114 AC: 171AN: 149610Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000313 AC: 66AN: 211150Hom.: 0 AF XY: 0.000244 AC XY: 28AN XY: 114690
GnomAD4 exome AF: 0.000124 AC: 178AN: 1437614Hom.: 0 AF XY: 0.000130 AC XY: 93AN XY: 713570
GnomAD4 genome AF: 0.00114 AC: 171AN: 149726Hom.: 0 Cov.: 32 AF XY: 0.00119 AC XY: 87AN XY: 73102
ClinVar
Submissions by phenotype
not provided Benign:5
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 23, 2020 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | PCDH15: BS1 - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 25, 2017 | p.Pro1760_Pro1762del in exon 33 of PCDH15: This variant is not expected to have clinical significance because it has been identified in 0.4% (77/20736) of Afric an chromosomes by the Genome Aggregation Database (gnomAD, http://exac.broadinst itute.org; dbSNP rs373916538). - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 03, 2017 | - - |
PCDH15-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 10, 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, criteria provided, single submitter | clinical testing | Counsyl | Mar 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at