10-54189391-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142769.3(PCDH15):c.1321-7C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000111 in 1,526,648 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001142769.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000320301.11 | c.1306-4123C>A | intron_variant | Intron 11 of 32 | 1 | NM_033056.4 | ENSP00000322604.6 | |||
PCDH15 | ENST00000644397.2 | c.1306-4123C>A | intron_variant | Intron 11 of 37 | NM_001384140.1 | ENSP00000495195.1 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151726Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000117 AC: 2AN: 170490Hom.: 0 AF XY: 0.0000110 AC XY: 1AN XY: 91120
GnomAD4 exome AF: 0.0000116 AC: 16AN: 1374922Hom.: 0 Cov.: 27 AF XY: 0.00000882 AC XY: 6AN XY: 680356
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151726Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74076
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at