16-31126391-C-T

Position:

• chr16-31126391-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032188.3(KAT8):​c.463-644C>T variant causes a intron 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 NM_032188.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.87

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
KAT8	NM_032188.3	c.463-644C>T		intron_variant		ENST00000219797.9	NP_115564.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KAT8	ENST00000219797.9	c.463-644C>T		intron_variant		1	NM_032188.3	ENSP00000219797.3
KAT8	ENST00000448516.6	c.463-644C>T		intron_variant		1		ENSP00000406037.2
KAT8	ENST00000538768.2	n.808C>T		non_coding_transcript_exon_variant	1/8	1
KAT8	ENST00000543774.6	c.463-644C>T		intron_variant		5		ENSP00000456933.2

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48378 AN: 151886 Hom.: 9682 Cov.: 32

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.: 31 Cov.: 0 AF XY: 0.301 AC XY: 106 AN XY: 352

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.389

Gnomad4 ASJ exome AF: 0.833

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.122

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.308

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.318 AC: 48386 AN: 152004 Hom.: 9685 Cov.: 32 AF XY: 0.321 AC XY: 23866 AN XY: 74258

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.380

Alfa AF: 0.364 Hom.: 7561

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
DANN	Benign	0.47

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

Other links and lift over

dbSNP: rs889548; hg19: chr16-31137712;