Variant 10-75020544-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_012330.4(KAT6B):c.2630-38C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0416 in 1,421,902 control chromosomes in the GnomAD database, including 3,289 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.030 ( 232 hom., cov: 32)

Exomes 𝑓: 0.043 ( 3057 hom. )

Consequence

KAT6B
NM_012330.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.103

Variant links:

Genes affected

KAT6B (HGNC:17582): (lysine acetyltransferase 6B) The protein encoded by this gene is a histone acetyltransferase and component of the MOZ/MORF protein complex. In addition to its acetyltransferase activity, the encoded protein has transcriptional activation activity in its N-terminal end and transcriptional repression activity in its C-terminal end. This protein is necessary for RUNX2-dependent transcriptional activation and could be involved in brain development. Mutations have been found in patients with genitopatellar syndrome. A translocation of this gene and the CREBBP gene results in acute myeloid leukemias. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]

KAT6B links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 10-75020544-C-T is Benign according to our data. Variant chr10-75020544-C-T is described in ClinVar as [Benign]. Clinvar id is 1250408.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KAT6B	NM_012330.4 linkuse as main transcript	c.2630-38C>T		intron_variant		ENST00000287239.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KAT6B	ENST00000287239.10 linkuse as main transcript	c.2630-38C>T		intron_variant		1	NM_012330.4	P2	Q8WYB5-1
	ENST00000413431.1 linkuse as main transcript	n.65+4566G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0295

AC:

4495

AN:

152186

Hom.:

232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00589

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0206

Gnomad ASJ

AF:

0.0447

Gnomad EAS

AF:

0.0652

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.0216

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0288

Gnomad OTH

AF:

0.0258

GnomAD3 exomes

AF:

0.0544

AC:

13459

AN:

247462

Hom.:

1083

AF XY:

0.0638

AC XY:

8560

AN XY:

134156

show subpopulations

Gnomad AFR exome

AF:

0.00442

Gnomad AMR exome

AF:

0.0156

Gnomad ASJ exome

AF:

0.0457

Gnomad EAS exome

AF:

0.0717

Gnomad SAS exome

AF:

0.240

Gnomad FIN exome

AF:

0.0200

Gnomad NFE exome

AF:

0.0279

Gnomad OTH exome

AF:

0.0431

GnomAD4 exome

AF:

0.0430

AC:

54656

AN:

1269598

Hom.:

3057

Cov.:

AF XY:

0.0492

AC XY:

31534

AN XY:

641466

show subpopulations

Gnomad4 AFR exome

AF:

0.00500

Gnomad4 AMR exome

AF:

0.0163

Gnomad4 ASJ exome

AF:

0.0437

Gnomad4 EAS exome

AF:

0.0696

Gnomad4 SAS exome

AF:

0.230

Gnomad4 FIN exome

AF:

0.0204

Gnomad4 NFE exome

AF:

0.0291

Gnomad4 OTH exome

AF:

0.0456

GnomAD4 genome

AF:

0.0295

AC:

4496

AN:

152304

Hom.:

232

Cov.:

AF XY:

0.0331

AC XY:

2465

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00587

Gnomad4 AMR

AF:

0.0206

Gnomad4 ASJ

AF:

0.0447

Gnomad4 EAS

AF:

0.0654

Gnomad4 SAS

AF:

0.246

Gnomad4 FIN

AF:

0.0216

Gnomad4 NFE

AF:

0.0288

Gnomad4 OTH

AF:

0.0255

Alfa

AF:

0.0229

Hom.:

Bravo

AF:

0.0227

Asia WGS

AF:

0.142

AC:

493

AN:

3478

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 submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.7

DANN

Benign

0.48

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over