11-65713695-T-C

Variant names:

• chr11-65713695-T-C
• rs1151500
• NM_182710.3:c.615+28T>C

Variant summary

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

The NM_182710.3(KAT5):​c.615+28T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 1,613,820 control chromosomes in the GnomAD database, including 648,203 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 0.86 (56950 hom., cov: 31)
  • Exomes 𝑓: 0.90 (591253 hom.)
• Consequence: KAT5 NM_182710.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

Genes affected

KAT5 (HGNC:5275): (lysine acetyltransferase 5) The protein encoded by this gene belongs to the MYST family of histone acetyl transferases (HATs) and was originally isolated as an HIV-1 TAT-interactive protein. HATs play important roles in regulating chromatin remodeling, transcription and other nuclear processes by acetylating histone and nonhistone proteins. This protein is a histone acetylase that has a role in DNA repair and apoptosis and is thought to play an important role in signal transduction. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KAT5	NM_182710.3	c.615+28T>C		intron_variant	Intron 5 of 12	ENST00000341318.9	NP_874369.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KAT5	ENST00000341318.9	c.615+28T>C		intron_variant	Intron 5 of 12	1	NM_182710.3	ENSP00000340330.4

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131186 AN: 152094 Hom.: 56911 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.871

GnomAD3 exomes AF: 0.870 AC: 218784 AN: 251376 Hom.: 95860 AF XY: 0.867 AC XY: 117806 AN XY: 135852

Gnomad AFR exome AF: 0.765

Gnomad AMR exome AF: 0.864

Gnomad ASJ exome AF: 0.885

Gnomad EAS exome AF: 0.897

Gnomad SAS exome AF: 0.721

Gnomad FIN exome AF: 0.903

Gnomad NFE exome AF: 0.915

Gnomad OTH exome AF: 0.894

GnomAD4 exome AF: 0.898 AC: 1312306 AN: 1461608 Hom.: 591253 Cov.: 42 AF XY: 0.894 AC XY: 649874 AN XY: 727132

Gnomad4 AFR exome AF: 0.766

Gnomad4 AMR exome AF: 0.866

Gnomad4 ASJ exome AF: 0.884

Gnomad4 EAS exome AF: 0.894

Gnomad4 SAS exome AF: 0.728

Gnomad4 FIN exome AF: 0.903

Gnomad4 NFE exome AF: 0.917

Gnomad4 OTH exome AF: 0.890

GnomAD4 genome AF: 0.863 AC: 131286 AN: 152212 Hom.: 56950 Cov.: 31 AF XY: 0.861 AC XY: 64060 AN XY: 74430

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.916

Gnomad4 OTH AF: 0.869

Alfa AF: 0.901 Hom.: 86432

Bravo AF: 0.859

Asia WGS AF: 0.793 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.27

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1151500; hg19: chr11-65481166;