Genetic Variant KAT8:n.808C>T (chr16-31126391-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000538768.2(KAT8):n.808C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,518 control chromosomes in the GnomAD database, including 9,716 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.32 ( 9685 hom., cov: 32)

Exomes 𝑓: 0.30 ( 31 hom. )

Consequence

KAT8
ENST00000538768.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.87

Publications

34 publications found

Variant links:

Genes affected

KAT8 (HGNC:17933): (lysine acetyltransferase 8) This gene encodes a member of the MYST histone acetylase protein family. The encoded protein has a characteristic MYST domain containing an acetyl-CoA-binding site, a chromodomain typical of proteins which bind histones, and a C2HC-type zinc finger. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

KAT8 Gene-Disease associations (from GenCC):

Li-Ghorbani-Weisz-Hubshman syndrome
Inheritance: AR, AD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

KAT8 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KAT8	NM_032188.3 link	c.463-644C>T		intron_variant	Intron 3 of 10	ENST00000219797.9	NP_115564.2	Q9H7Z6-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
KAT8	ENST00000538768.2 link	n.808C>T	non_coding_transcript_exon_variant	Exon 1 of 8	1
KAT8	ENST00000219797.9 link	c.463-644C>T	intron_variant	Intron 3 of 10	1	NM_032188.3	ENSP00000219797.3	Q9H7Z6-1
KAT8	ENST00000448516.6 link	c.463-644C>T	intron_variant	Intron 3 of 9	1		ENSP00000406037.2	Q9H7Z6-2
KAT8	ENST00000543774.6 link	c.463-644C>T	intron_variant	Intron 4 of 11	5		ENSP00000456933.2	Q9H7Z6-1

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48378

AN:

151886

Hom.:

9682

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.436

Gnomad AMR

AF:

0.380

Gnomad ASJ

AF:

0.496

Gnomad EAS

AF:

0.891

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.391

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.364

Gnomad OTH

AF:

0.382

GnomAD4 exome

AF:

0.298

AC:

153

AN:

514

Hom.:

Cov.:

AF XY:

0.301

AC XY:

106

AN XY:

352

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.389

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.833

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.122

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.308

AC:

112

AN:

364

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

GnomAD4 genome

AF:

0.318

AC:

48386

AN:

152004

Hom.:

9685

Cov.:

AF XY:

0.321

AC XY:

23866

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.125

AC:

5188

AN:

41462

American (AMR)

AF:

0.380

AC:

5807

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.496

AC:

1721

AN:

3470

East Asian (EAS)

AF:

0.891

AC:

4607

AN:

5168

South Asian (SAS)

AF:

0.177

AC:

852

AN:

4818

European-Finnish (FIN)

AF:

0.391

AC:

4128

AN:

10552

Middle Eastern (MID)

AF:

0.527

AC:

155

AN:

294

European-Non Finnish (NFE)

AF:

0.364

AC:

24729

AN:

67952

Other (OTH)

AF:

0.380

AC:

802

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1518

3037

4555

6074

7592

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

464

928

1392

1856

2320

<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:

0.364

Hom.:

8417

Bravo

AF:

0.322

Asia WGS

AF:

0.463

AC:

1614

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.030

(source)

DANN

Benign

0.47

PhyloP100

-3.9

Mutation Taster

=100/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over