rs57372986
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_012330.4(KAT6B):c.3649G>T(p.Ala1217Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00128 in 1,614,156 control chromosomes in the GnomAD database, including 17 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 (★★).
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.3649G>T | p.Ala1217Ser | missense_variant | 17/18 | ENST00000287239.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAT6B | ENST00000287239.10 | c.3649G>T | p.Ala1217Ser | missense_variant | 17/18 | 1 | NM_012330.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00627 AC: 954AN: 152234Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00159 AC: 400AN: 250962Hom.: 4 AF XY: 0.00119 AC XY: 162AN XY: 135700
GnomAD4 exome AF: 0.000769 AC: 1124AN: 1461804Hom.: 7 Cov.: 31 AF XY: 0.000688 AC XY: 500AN XY: 727210
GnomAD4 genome ? AF: 0.00624 AC: 950AN: 152352Hom.: 10 Cov.: 32 AF XY: 0.00588 AC XY: 438AN XY: 74506
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2017 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 27, 2018 | p.Ala1217Ser in exon 17 of KAT6B: This variant is not expected to have clinical significance because it has been identified in 2.08% (212/10216) of African chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs57372986). - |
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