8-41932248-C-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS2
The NM_006766.5(KAT6A):c.5972G>T(p.Gly1991Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,460,892 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
KAT6A
NM_006766.5 missense
NM_006766.5 missense
Scores
6
9
4
Clinical Significance
Conservation
PhyloP100: 5.77
Genes affected
KAT6A (HGNC:13013): (lysine acetyltransferase 6A) This gene encodes a member of the MOZ, YBFR2, SAS2, TIP60 family of histone acetyltransferases. The protein is composed of a nuclear localization domain, a double C2H2 zinc finger domain that binds to acetylated histone tails, a histone acetyl-transferase domain, a glutamate/aspartate-rich region, and a serine- and methionine-rich transactivation domain. It is part of a complex that acetylates lysine-9 residues in histone 3, and in addition, it acts as a co-activator for several transcription factors. Allelic variants of this gene are associated with an autosomal dominant form of cognitive disability. Chromosomal translocations of this gene are associated with acute myeloid leukemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 8-41932248-C-A is Benign according to our data. Variant chr8-41932248-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2879433.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 5 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KAT6A | ENST00000265713.8 | c.5972G>T | p.Gly1991Val | missense_variant | 17/17 | 1 | NM_006766.5 | ENSP00000265713.2 | ||
KAT6A | ENST00000406337.6 | c.5978G>T | p.Gly1993Val | missense_variant | 18/18 | 5 | ENSP00000385888.2 | |||
KAT6A | ENST00000396930.4 | c.5972G>T | p.Gly1991Val | missense_variant | 18/18 | 5 | ENSP00000380136.3 | |||
KAT6A | ENST00000649817.1 | c.4652G>T | p.Gly1551Val | missense_variant | 11/11 | ENSP00000497780.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249976Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 135018
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460892Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726694
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 05, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
.;D;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.;T
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Benign
.;L;L
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
.;D;D
REVEL
Uncertain
Sift
Pathogenic
.;D;D
Sift4G
Pathogenic
.;D;D
Polyphen
1.0
.;D;D
Vest4
0.88, 0.82
MutPred
0.30
.;Gain of helix (P = 0.062);Gain of helix (P = 0.062);
MVP
MPC
0.24
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at