rs201202020
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_001329943.3(KIAA0586):āc.3663T>Gā(p.Ser1221=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,613,946 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001329943.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA0586 | NM_001329943.3 | c.3663T>G | p.Ser1221= | synonymous_variant | 24/31 | ENST00000652326.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0586 | ENST00000652326.2 | c.3663T>G | p.Ser1221= | synonymous_variant | 24/31 | NM_001329943.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000848 AC: 129AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000891 AC: 222AN: 249060Hom.: 0 AF XY: 0.000999 AC XY: 135AN XY: 135102
GnomAD4 exome AF: 0.00111 AC: 1616AN: 1461644Hom.: 0 Cov.: 31 AF XY: 0.00109 AC XY: 795AN XY: 727104
GnomAD4 genome ? AF: 0.000847 AC: 129AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000846 AC XY: 63AN XY: 74468
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 07, 2023 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown. - |
Joubert syndrome 23;C4225286:Short-rib thoracic dysplasia 14 with polydactyly Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
KIAA0586-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 06, 2020 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at