NM_012330.4:c.3310_3312dupGAA

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP3BP6_Very_StrongBS2

The NM_012330.4(KAT6B):c.3310_3312dupGAA(p.Glu1104dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00636 in 1,605,902 control chromosomes in the GnomAD database, including 21 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0053 ( 2 hom., cov: 22)

Exomes 𝑓: 0.0065 ( 19 hom. )

Consequence

KAT6B
NM_012330.4 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 3.08

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 -13 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_012330.4

BP6

Variant 10-75022147-G-GGAA is Benign according to our data. Variant chr10-75022147-G-GGAA is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 260238.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 801 AD gene.

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_3312dupGAA	p.Glu1104dup	conservative_inframe_insertion	Exon 16 of 18	NP_036462.2	Q8WYB5-1
KAT6B	NM_001370136.1		c.3310_3312dupGAA	p.Glu1104dup	conservative_inframe_insertion	Exon 16 of 18	NP_001357065.1	Q8WYB5-1
KAT6B	NM_001370137.1		c.3310_3312dupGAA	p.Glu1104dup	conservative_inframe_insertion	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_3312dupGAA	p.Glu1104dup	conservative_inframe_insertion	Exon 16 of 18	ENSP00000287239.4	Q8WYB5-1
KAT6B	ENST00000372711.2	TSL:1	c.2761_2763dupGAA	p.Glu921dup	conservative_inframe_insertion	Exon 16 of 18	ENSP00000361796.1	Q8WYB5-2
KAT6B	ENST00000648725.1		c.3310_3312dupGAA	p.Glu1104dup	conservative_inframe_insertion	Exon 16 of 18	ENSP00000497841.1	Q8WYB5-1

Frequencies

GnomAD3 genomes

AF:

0.00535

AC:

803

AN:

150036

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00146

Gnomad AMI

AF:

0.0881

Gnomad AMR

AF:

0.00697

Gnomad ASJ

AF:

0.00549

Gnomad EAS

AF:

0.000196

Gnomad SAS

AF:

0.00191

Gnomad FIN

AF:

0.00250

Gnomad MID

AF:

0.0128

Gnomad NFE

AF:

0.00727

Gnomad OTH

AF:

0.00389

GnomAD2 exomes

AF:

0.00505

AC:

1203

AN:

238206

AF XY:

0.00512

show subpopulations

Gnomad AFR exome

AF:

0.000946

Gnomad AMR exome

AF:

0.00453

Gnomad ASJ exome

AF:

0.00358

Gnomad EAS exome

AF:

0.000168

Gnomad FIN exome

AF:

0.00298

Gnomad NFE exome

AF:

0.00807

Gnomad OTH exome

AF:

0.00455

GnomAD4 exome

AF:

0.00646

AC:

9410

AN:

1455750

Hom.:

Cov.:

AF XY:

0.00649

AC XY:

4704

AN XY:

724420

show subpopulations

African (AFR)

AF:

0.000819

AC:

AN:

32966

American (AMR)

AF:

0.00426

AC:

190

AN:

44640

Ashkenazi Jewish (ASJ)

AF:

0.00372

AC:

AN:

26104

East Asian (EAS)

AF:

0.000227

AC:

AN:

39604

South Asian (SAS)

AF:

0.00159

AC:

137

AN:

85948

European-Finnish (FIN)

AF:

0.00328

AC:

174

AN:

52986

Middle Eastern (MID)

AF:

0.00382

AC:

AN:

5760

European-Non Finnish (NFE)

AF:

0.00760

AC:

8414

AN:

1107538

Other (OTH)

AF:

0.00565

AC:

340

AN:

60204

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

435

870

1306

1741

2176

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

306

612

918

1224

1530

<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:

0.00533

AC:

801

AN:

150152

Hom.:

Cov.:

AF XY:

0.00517

AC XY:

379

AN XY:

73298

show subpopulations

African (AFR)

AF:

0.00146

AC:

AN:

40540

American (AMR)

AF:

0.00696

AC:

105

AN:

15076

Ashkenazi Jewish (ASJ)

AF:

0.00549

AC:

AN:

3462

East Asian (EAS)

AF:

0.000197

AC:

AN:

5086

South Asian (SAS)

AF:

0.00192

AC:

AN:

4698

European-Finnish (FIN)

AF:

0.00250

AC:

AN:

10390

Middle Eastern (MID)

AF:

0.00690

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.00728

AC:

492

AN:

67626

Other (OTH)

AF:

0.00385

AC:

AN:

2076

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

103

138

172

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00281

Hom.:

213

ClinVar

ClinVar submissions

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (4)

not specified (3)

Genitopatellar syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.1

Mutation Taster

=84/16

polymorphism

(source)

Splicing

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