rs5785040
Positions:
- chr10-54132840-TACACACAC-T
- chr10-54132840-TACACACAC-TAC
- chr10-54132840-TACACACAC-TACAC
- chr10-54132840-TACACACAC-TACACAC
- chr10-54132840-TACACACAC-TACACACACAC
- chr10-54132840-TACACACAC-TACACACACACAC
- chr10-54132840-TACACACAC-TACACACACACACAC
- chr10-54132840-TACACACAC-TACACACACACACACAC
- chr10-54132840-TACACACAC-TACACACACACACACACAC
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_033056.4(PCDH15):c.1917+27_1917+34del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000601 in 1,496,272 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000059 ( 0 hom. )
Consequence
PCDH15
NM_033056.4 intron
NM_033056.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.22
Genes affected
PCDH15 (HGNC:14674): (protocadherin related 15) This gene is a member of the cadherin superfamily. Family members encode integral membrane proteins that mediate calcium-dependent cell-cell adhesion. It plays an essential role in maintenance of normal retinal and cochlear function. Mutations in this gene result in hearing loss and Usher Syndrome Type IF (USH1F). Extensive alternative splicing resulting in multiple isoforms has been observed in the mouse ortholog. Similar alternatively spliced transcripts are inferred to occur in human, and additional variants are likely to occur. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH15 | NM_001384140.1 | c.1917+27_1917+34del | intron_variant | ENST00000644397.2 | |||
PCDH15 | NM_033056.4 | c.1917+27_1917+34del | intron_variant | ENST00000320301.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000320301.11 | c.1917+27_1917+34del | intron_variant | 1 | NM_033056.4 | ||||
PCDH15 | ENST00000644397.2 | c.1917+27_1917+34del | intron_variant | NM_001384140.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000665 AC: 1AN: 150402Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00000594 AC: 8AN: 1345762Hom.: 0 AF XY: 0.00000900 AC XY: 6AN XY: 666798
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ClinVar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at