rs61735441
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014804.3(KIAA0753):āc.1756A>Gā(p.Lys586Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00893 in 1,568,062 control chromosomes in the GnomAD database, including 93 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_014804.3 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 |
---|---|---|---|---|---|---|---|
KIAA0753 | NM_014804.3 | c.1756A>G | p.Lys586Glu | missense_variant | 10/19 | ENST00000361413.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0753 | ENST00000361413.8 | c.1756A>G | p.Lys586Glu | missense_variant | 10/19 | 1 | NM_014804.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00709 AC: 1079AN: 152208Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00711 AC: 1626AN: 228834Hom.: 8 AF XY: 0.00683 AC XY: 854AN XY: 125032
GnomAD4 exome AF: 0.00912 AC: 12916AN: 1415736Hom.: 91 Cov.: 29 AF XY: 0.00892 AC XY: 6286AN XY: 704438
GnomAD4 genome ? AF: 0.00708 AC: 1079AN: 152326Hom.: 2 Cov.: 33 AF XY: 0.00708 AC XY: 527AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 26, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | KIAA0753: BP4, BS2 - |
Orofaciodigital syndrome XV;C5561958:Joubert syndrome 38;C5561961:Short-rib thoracic dysplasia 21 without polydactyly Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 26, 2022 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at