chr14-58427647-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000619416.4(KIAA0586):c.-39+10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000145 in 1,383,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
KIAA0586
ENST00000619416.4 intron
ENST00000619416.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.400
Genes affected
KIAA0586 (HGNC:19960): (KIAA0586) This gene encodes a conserved centrosomal protein that functions in ciliogenesis and responds to hedgehog signaling. Mutations in this gene causes Joubert syndrome 23. Alternative splicing results in multiple transcript variants and protein isoforms. [provided by RefSeq, Aug 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA0586 | NM_001244189.2 | c.9+10T>C | intron_variant | ||||
KIAA0586 | NM_001244190.2 | c.-39+10T>C | intron_variant | ||||
KIAA0586 | NM_001244191.2 | c.-57+10T>C | intron_variant | ||||
KIAA0586 | NM_001244192.2 | c.-57+10T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0586 | ENST00000423743.7 | c.-57+10T>C | intron_variant | 1 | |||||
KIAA0586 | ENST00000619416.4 | c.-39+10T>C | intron_variant | 1 | A2 | ||||
KIAA0586 | ENST00000354386.10 | c.9+10T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000145 AC: 2AN: 1383374Hom.: 0 Cov.: 30 AF XY: 0.00000293 AC XY: 2AN XY: 682584
GnomAD4 exome
AF:
AC:
2
AN:
1383374
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Cov.:
30
AF XY:
AC XY:
2
AN XY:
682584
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
KIAA0586-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 29, 2024 | The KIAA0586 c.9+10T>C variant is predicted to interfere with splicing. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. However, the use of computer prediction programs is not equivalent to functional evidence, and therefore the clinical significance of this variant is uncertain. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.