chr20-18187333-C-T

Position:

• chr20-18187333-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BS1 BS2

The NM_001392073.1(KAT14):​c.2220C>T​(p.Pro740=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0164 in 1,613,928 control chromosomes in the GnomAD database, including 269 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 0.014 (22 hom., cov: 33)
  • Exomes 𝑓: 0.017 (247 hom.)
• Consequence: KAT14 NM_001392073.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.97

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=-0.9).
• BP7: Synonymous conserved (PhyloP=-4.97 with no splicing effect.
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.014 (2136/152332) while in subpopulation AMR AF= 0.0214 (328/15308). AF 95% confidence interval is 0.0195. There are 22 homozygotes in gnomad4. There are 1081 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 22 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KAT14	NM_001392073.1	c.2220C>T	p.Pro740=	synonymous_variant	11/11	ENST00000688188.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KAT14	ENST00000688188.1	c.2220C>T	p.Pro740=	synonymous_variant	11/11		NM_001392073.1	A1

Frequencies

GnomAD3 genomes AF: 0.0140 AC: 2136 AN: 152214 Hom.: 22 Cov.: 33

Gnomad AFR AF: 0.00425

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0215

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00517

Gnomad FIN AF: 0.0144

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.0172

GnomAD4 exome AF: 0.0167 AC: 24390 AN: 1461596 Hom.: 247 Cov.: 31 AF XY: 0.0165 AC XY: 12022 AN XY: 727080

Gnomad4 AFR exome AF: 0.00368

Gnomad4 AMR exome AF: 0.0119

Gnomad4 ASJ exome AF: 0.0276

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00429

Gnomad4 FIN exome AF: 0.0154

Gnomad4 NFE exome AF: 0.0186

Gnomad4 OTH exome AF: 0.0157

GnomAD4 genome AF: 0.0140 AC: 2136 AN: 152332 Hom.: 22 Cov.: 33 AF XY: 0.0145 AC XY: 1081 AN XY: 74492

Gnomad4 AFR AF: 0.00423

Gnomad4 AMR AF: 0.0214

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00518

Gnomad4 FIN AF: 0.0144

Gnomad4 NFE AF: 0.0192

Gnomad4 OTH AF: 0.0170

Alfa AF: 0.0187 Hom.: 16

Bravo AF: 0.0140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2747404; hg19: chr20-18167977;