rs199732899
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001329943.3(KIAA0586):c.4430-6A>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,517,328 control chromosomes in the GnomAD database, including 1 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 Likely benign (★).
Frequency
Consequence
NM_001329943.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA0586 | NM_001329943.3 | c.4430-6A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000652326.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0586 | ENST00000652326.2 | c.4430-6A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001329943.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000743 AC: 113AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000650 AC: 108AN: 166228Hom.: 0 AF XY: 0.000696 AC XY: 61AN XY: 87604
GnomAD4 exome AF: 0.00113 AC: 1539AN: 1365054Hom.: 1 Cov.: 23 AF XY: 0.00104 AC XY: 703AN XY: 675976
GnomAD4 genome ? AF: 0.000742 AC: 113AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000765 AC XY: 57AN XY: 74472
ClinVar
Submissions by phenotype
Joubert syndrome 23;C4225286:Short-rib thoracic dysplasia 14 with polydactyly Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at