chr10-75022147-GGAA-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP3BP6_Very_StrongBA1

The NM_012330.4(KAT6B):c.3310_3312delGAA(p.Glu1104del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.177 in 1,596,330 control chromosomes in the GnomAD database, including 43,575 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 13474 hom., cov: 22)

Exomes 𝑓: 0.16 ( 30101 hom. )

Consequence

KAT6B
NM_012330.4 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 4.43

Publications

23 publications found

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 Gene-Disease associations (from GenCC):

blepharophimosis - intellectual disability syndrome, SBBYS type
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet
genitopatellar syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
KAT6B-related multiple congenital anomalies syndrome
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
multiple congenital anomalies/dysmorphic syndrome
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
RASopathy
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

KAT6B links:

ENSG00000234149 (HGNC:):

ENSG00000234149 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_012330.4

BP6

Variant 10-75022147-GGAA-G is Benign according to our data. Variant chr10-75022147-GGAA-G is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 211214.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012330.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
KAT6B	NM_012330.4	MANE Select	c.3310_3312delGAA	p.Glu1104del	conservative_inframe_deletion	Exon 16 of 18	NP_036462.2	Q8WYB5-1
KAT6B	NM_001370136.1		c.3310_3312delGAA	p.Glu1104del	conservative_inframe_deletion	Exon 16 of 18	NP_001357065.1	Q8WYB5-1
KAT6B	NM_001370137.1		c.3310_3312delGAA	p.Glu1104del	conservative_inframe_deletion	Exon 16 of 18	NP_001357066.1	Q8WYB5-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
KAT6B	ENST00000287239.10	TSL:1 MANE Select	c.3310_3312delGAA	p.Glu1104del	conservative_inframe_deletion	Exon 16 of 18	ENSP00000287239.4	Q8WYB5-1
KAT6B	ENST00000372711.2	TSL:1	c.2761_2763delGAA	p.Glu921del	conservative_inframe_deletion	Exon 16 of 18	ENSP00000361796.1	Q8WYB5-2
KAT6B	ENST00000648725.1		c.3310_3312delGAA	p.Glu1104del	conservative_inframe_deletion	Exon 16 of 18	ENSP00000497841.1	Q8WYB5-1

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

47842

AN:

149910

Hom.:

13423

Cov.:

show subpopulations

Gnomad AFR

AF:

0.752

Gnomad AMI

AF:

0.0297

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.0842

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.275

GnomAD2 exomes

AF:

0.237

AC:

56520

AN:

238206

AF XY:

0.230

show subpopulations

Gnomad AFR exome

AF:

0.755

Gnomad AMR exome

AF:

0.299

Gnomad ASJ exome

AF:

0.169

Gnomad EAS exome

AF:

0.357

Gnomad FIN exome

AF:

0.0855

Gnomad NFE exome

AF:

0.117

Gnomad OTH exome

AF:

0.190

GnomAD4 exome

AF:

0.162

AC:

234276

AN:

1446304

Hom.:

30101

AF XY:

0.166

AC XY:

119677

AN XY:

719950

show subpopulations

African (AFR)

AF:

0.763

AC:

25126

AN:

32946

American (AMR)

AF:

0.291

AC:

12974

AN:

44544

Ashkenazi Jewish (ASJ)

AF:

0.164

AC:

4272

AN:

25980

East Asian (EAS)

AF:

0.387

AC:

15313

AN:

39522

South Asian (SAS)

AF:

0.389

AC:

33343

AN:

85682

European-Finnish (FIN)

AF:

0.0863

AC:

4558

AN:

52794

Middle Eastern (MID)

AF:

0.227

AC:

1303

AN:

5746

European-Non Finnish (NFE)

AF:

0.114

AC:

125691

AN:

1099232

Other (OTH)

AF:

0.195

AC:

11696

AN:

59858

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

9606

19212

28819

38425

48031

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5256

10512

15768

21024

26280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.320

AC:

47948

AN:

150026

Hom.:

13474

Cov.:

AF XY:

0.317

AC XY:

23218

AN XY:

73242

show subpopulations

African (AFR)

AF:

0.752

AC:

30449

AN:

40486

American (AMR)

AF:

0.247

AC:

3721

AN:

15054

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

572

AN:

3462

East Asian (EAS)

AF:

0.356

AC:

1810

AN:

5086

South Asian (SAS)

AF:

0.430

AC:

2015

AN:

4686

European-Finnish (FIN)

AF:

0.0842

AC:

873

AN:

10372

Middle Eastern (MID)

AF:

0.259

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.116

AC:

7839

AN:

67610

Other (OTH)

AF:

0.274

AC:

567

AN:

2072

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

965

1930

2896

3861

4826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

414

828

1242

1656

2070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0981

Hom.:

213

Bravo

AF:

0.348

ClinVar

ClinVar submissions

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (5)

not provided (3)

Genitopatellar syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.4

Mutation Taster

=81/19

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over