rs141632537
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_014804.3(KIAA0753):c.754C>T(p.Arg252Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000729 in 1,561,708 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R252H) has been classified as Uncertain significance.
Frequency
Consequence
NM_014804.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA0753 | NM_014804.3 | c.754C>T | p.Arg252Cys | missense_variant | 4/19 | ENST00000361413.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0753 | ENST00000361413.8 | c.754C>T | p.Arg252Cys | missense_variant | 4/19 | 1 | NM_014804.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00310 AC: 471AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000867 AC: 149AN: 171824Hom.: 0 AF XY: 0.000602 AC XY: 55AN XY: 91324
GnomAD4 exome AF: 0.000473 AC: 666AN: 1409440Hom.: 1 Cov.: 30 AF XY: 0.000412 AC XY: 287AN XY: 696116
GnomAD4 genome AF: 0.00310 AC: 472AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.00281 AC XY: 209AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 19, 2017 | - - |
KIAA0753-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 18, 2019 | This variant is classified as 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