10-75029319-G-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_012330.4(KAT6B):c.4495G>A(p.Val1499Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0178 in 1,614,038 control chromosomes in the GnomAD database, including 685 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 Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1499T) has been classified as Uncertain significance.
Frequency
Consequence
NM_012330.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAT6B | NM_012330.4 | c.4495G>A | p.Val1499Ile | missense_variant | 18/18 | ENST00000287239.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAT6B | ENST00000287239.10 | c.4495G>A | p.Val1499Ile | missense_variant | 18/18 | 1 | NM_012330.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0324 AC: 4920AN: 152032Hom.: 142 Cov.: 32
GnomAD3 exomes AF: 0.0349 AC: 8755AN: 251050Hom.: 300 AF XY: 0.0316 AC XY: 4289AN XY: 135714
GnomAD4 exome AF: 0.0163 AC: 23770AN: 1461888Hom.: 543 Cov.: 35 AF XY: 0.0163 AC XY: 11825AN XY: 727246
GnomAD4 genome AF: 0.0323 AC: 4922AN: 152150Hom.: 142 Cov.: 32 AF XY: 0.0337 AC XY: 2508AN XY: 74400
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 11, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Genitopatellar syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at