20-18162711-C-T

Position:

• chr20-18162711-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001392073.1(KAT14):​c.1434C>T​(p.Pro478Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,614,012 control chromosomes in the GnomAD database, including 63,983 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 0.23 (4817 hom., cov: 33)
  • Exomes 𝑓: 0.27 (59166 hom.)
• Consequence: KAT14 NM_001392073.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

Genes affected

KAT14 (HGNC:15904): (lysine acetyltransferase 14) CSRP2 is a protein containing two LIM domains, which are double zinc finger motifs found in proteins of diverse function. CSRP2 and some related proteins are thought to act as protein adapters, bridging two or more proteins to form a larger protein complex. The protein encoded by this gene binds to one of the LIM domains of CSRP2 and contains an acetyltransferase domain. Although the encoded protein has been detected in the cytoplasm, it is predominantly a nuclear protein. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jun 2011]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BP7: Synonymous conserved (PhyloP=-0.077 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KAT14	NM_001392073.1	c.1434C>T	p.Pro478Pro	synonymous_variant	7/11	ENST00000688188.1	NP_001379002.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KAT14	ENST00000688188.1	c.1434C>T	p.Pro478Pro	synonymous_variant	7/11		NM_001392073.1	ENSP00000508684.1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35101 AN: 152030 Hom.: 4815 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.206

GnomAD3 exomes AF: 0.291 AC: 72985 AN: 251180 Hom.: 11862 AF XY: 0.293 AC XY: 39825 AN XY: 135752

Gnomad AFR exome AF: 0.0937

Gnomad AMR exome AF: 0.317

Gnomad ASJ exome AF: 0.164

Gnomad EAS exome AF: 0.487

Gnomad SAS exome AF: 0.388

Gnomad FIN exome AF: 0.333

Gnomad NFE exome AF: 0.257

Gnomad OTH exome AF: 0.267

GnomAD4 exome AF: 0.275 AC: 401738 AN: 1461864 Hom.: 59166 Cov.: 43 AF XY: 0.278 AC XY: 202486 AN XY: 727224

Gnomad4 AFR exome AF: 0.0929

Gnomad4 AMR exome AF: 0.308

Gnomad4 ASJ exome AF: 0.165

Gnomad4 EAS exome AF: 0.552

Gnomad4 SAS exome AF: 0.385

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.261

Gnomad4 OTH exome AF: 0.270

GnomAD4 genome AF: 0.231 AC: 35103 AN: 152148 Hom.: 4817 Cov.: 33 AF XY: 0.238 AC XY: 17716 AN XY: 74376

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.205

Alfa AF: 0.247 Hom.: 8681

Bravo AF: 0.220

Asia WGS AF: 0.405 AC: 1405 AN: 3478

EpiCase AF: 0.245

EpiControl AF: 0.236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.4
DANN	Benign	0.73

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: rs1205194; hg19: chr20-18143355;