rs200556301
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_033056.4(PCDH15):c.3717+8G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000477 in 1,611,006 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_033056.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH15 | NM_001384140.1 | c.3717+8G>C | splice_region_variant, intron_variant | ENST00000644397.2 | |||
PCDH15 | NM_033056.4 | c.3717+8G>C | splice_region_variant, intron_variant | ENST00000320301.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000320301.11 | c.3717+8G>C | splice_region_variant, intron_variant | 1 | NM_033056.4 | ||||
PCDH15 | ENST00000644397.2 | c.3717+8G>C | splice_region_variant, intron_variant | NM_001384140.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00283 AC: 430AN: 152070Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000754 AC: 189AN: 250700Hom.: 6 AF XY: 0.000546 AC XY: 74AN XY: 135560
GnomAD4 exome AF: 0.000232 AC: 338AN: 1458820Hom.: 5 Cov.: 32 AF XY: 0.000196 AC XY: 142AN XY: 725860
GnomAD4 genome ? AF: 0.00283 AC: 431AN: 152186Hom.: 2 Cov.: 32 AF XY: 0.00292 AC XY: 217AN XY: 74412
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | 3717+8G>C in Intron 27 of PCDH15: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus seq uence and has been identified in 0.8% (31/3738) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.was hington.edu/EVS). - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 19, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 09, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at