rs61745119
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001329943.3(KIAA0586):c.1439C>T(p.Thr480Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00117 in 1,607,862 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001329943.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA0586 | NM_001329943.3 | c.1439C>T | p.Thr480Ile | missense_variant | 11/31 | ENST00000652326.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0586 | ENST00000652326.2 | c.1439C>T | p.Thr480Ile | missense_variant | 11/31 | NM_001329943.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00615 AC: 936AN: 152086Hom.: 10 Cov.: 33
GnomAD3 exomes AF: 0.00161 AC: 387AN: 239776Hom.: 4 AF XY: 0.00121 AC XY: 157AN XY: 129984
GnomAD4 exome AF: 0.000644 AC: 937AN: 1455658Hom.: 8 Cov.: 31 AF XY: 0.000597 AC XY: 432AN XY: 723620
GnomAD4 genome ? AF: 0.00618 AC: 941AN: 152204Hom.: 10 Cov.: 33 AF XY: 0.00599 AC XY: 446AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 14, 2021 | - - |
Joubert syndrome 23;C4225286:Short-rib thoracic dysplasia 14 with polydactyly Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at