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3-20072338-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_003884.5(KAT2B):c.309G>A(p.Glu103=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 1,610,800 control chromosomes in the GnomAD database, including 128,207 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.41 ( 13309 hom., cov: 31)
Exomes 𝑓: 0.39 ( 114898 hom. )

Consequence

KAT2B
NM_003884.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.375
Variant links:
Genes affected
KAT2B (HGNC:8638): (lysine acetyltransferase 2B) CBP and p300 are large nuclear proteins that bind to many sequence-specific factors involved in cell growth and/or differentiation, including c-jun and the adenoviral oncoprotein E1A. The protein encoded by this gene associates with p300/CBP. It has in vitro and in vivo binding activity with CBP and p300, and competes with E1A for binding sites in p300/CBP. It has histone acetyl transferase activity with core histones and nucleosome core particles, indicating that this protein plays a direct role in transcriptional regulation. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-20072338-G-A is Benign according to our data. Variant chr3-20072338-G-A is described in ClinVar as [Benign]. Clinvar id is 1258558.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.375 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KAT2BNM_003884.5 linkuse as main transcriptc.309G>A p.Glu103= synonymous_variant 2/18 ENST00000263754.5
KAT2BXM_005265528.5 linkuse as main transcriptc.309G>A p.Glu103= synonymous_variant 2/17
KAT2BXM_047449147.1 linkuse as main transcriptc.18G>A p.Glu6= synonymous_variant 4/20

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KAT2BENST00000263754.5 linkuse as main transcriptc.309G>A p.Glu103= synonymous_variant 2/181 NM_003884.5 P1
KAT2BENST00000426228.1 linkuse as main transcriptn.89G>A non_coding_transcript_exon_variant 2/54

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.414
AC:
62760
AN:
151760
Hom.:
13286
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.492
Gnomad AMI
AF:
0.284
Gnomad AMR
AF:
0.401
Gnomad ASJ
AF:
0.207
Gnomad EAS
AF:
0.428
Gnomad SAS
AF:
0.497
Gnomad FIN
AF:
0.393
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.379
Gnomad OTH
AF:
0.381
GnomAD3 exomes
AF:
0.399
AC:
100318
AN:
251290
Hom.:
20649
AF XY:
0.400
AC XY:
54264
AN XY:
135808
show subpopulations
Gnomad AFR exome
AF:
0.497
Gnomad AMR exome
AF:
0.379
Gnomad ASJ exome
AF:
0.215
Gnomad EAS exome
AF:
0.435
Gnomad SAS exome
AF:
0.483
Gnomad FIN exome
AF:
0.398
Gnomad NFE exome
AF:
0.381
Gnomad OTH exome
AF:
0.372
GnomAD4 exome
AF:
0.393
AC:
574001
AN:
1458922
Hom.:
114898
Cov.:
34
AF XY:
0.395
AC XY:
286888
AN XY:
725892
show subpopulations
Gnomad4 AFR exome
AF:
0.496
Gnomad4 AMR exome
AF:
0.386
Gnomad4 ASJ exome
AF:
0.217
Gnomad4 EAS exome
AF:
0.442
Gnomad4 SAS exome
AF:
0.481
Gnomad4 FIN exome
AF:
0.395
Gnomad4 NFE exome
AF:
0.387
Gnomad4 OTH exome
AF:
0.386
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.414
AC:
62825
AN:
151878
Hom.:
13309
Cov.:
31
AF XY:
0.415
AC XY:
30829
AN XY:
74200
show subpopulations
Gnomad4 AFR
AF:
0.493
Gnomad4 AMR
AF:
0.401
Gnomad4 ASJ
AF:
0.207
Gnomad4 EAS
AF:
0.429
Gnomad4 SAS
AF:
0.496
Gnomad4 FIN
AF:
0.393
Gnomad4 NFE
AF:
0.379
Gnomad4 OTH
AF:
0.377
Alfa
AF:
0.369
Hom.:
7651
Bravo
AF:
0.415
Asia WGS
AF:
0.441
AC:
1535
AN:
3478
EpiCase
AF:
0.365
EpiControl
AF:
0.355

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxSep 01, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
Cadd
Benign
8.0
Dann
Benign
0.52

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3021408; hg19: chr3-20113830; COSMIC: COSV55431227; API