14-58457939-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBS1BS2_Supporting
The NM_001329943.3(KIAA0586):c.1543G>A(p.Ala515Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000609 in 1,602,212 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001329943.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA0586 | NM_001329943.3 | c.1543G>A | p.Ala515Thr | missense_variant | 11/31 | ENST00000652326.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0586 | ENST00000652326.2 | c.1543G>A | p.Ala515Thr | missense_variant | 11/31 | NM_001329943.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000473 AC: 72AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00125 AC: 285AN: 228896Hom.: 2 AF XY: 0.00169 AC XY: 208AN XY: 123418
GnomAD4 exome AF: 0.000625 AC: 906AN: 1449912Hom.: 14 Cov.: 31 AF XY: 0.000911 AC XY: 656AN XY: 719830
GnomAD4 genome AF: 0.000460 AC: 70AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.000658 AC XY: 49AN XY: 74474
ClinVar
Submissions by phenotype
Joubert syndrome 23;C4225286:Short-rib thoracic dysplasia 14 with polydactyly Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at