chr20-18138018-C-T

Variant names:

• chr20-18138018-C-T
• rs184370918
• NM_001392073.1:c.-487C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Moderate BP6_Moderate BS2

The NM_001392073.1(KAT14):​c.-487C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00467 in 1,498,000 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0040 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0047 (22 hom.)
• Consequence: KAT14 NM_001392073.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.15

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]

PET117 (HGNC:40045): (PET117 cytochrome c oxidase chaperone) Predicted to be involved in mitochondrial cytochrome c oxidase assembly. Located in mitochondrion. Implicated in cytochrome-c oxidase deficiency disease. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BP6: Variant 20-18138018-C-T is Benign according to our data. Variant chr20-18138018-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2652219.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KAT14	NM_001392073.1	c.-487C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 11	ENST00000688188.1	NP_001379002.1
PET117	NM_001164811.2	c.63C>T	p.Ala21Ala	synonymous_variant	Exon 1 of 2	ENST00000432901.4	NP_001158283.1
KAT14	NM_001392073.1	c.-487C>T		5_prime_UTR_variant	Exon 1 of 11	ENST00000688188.1	NP_001379002.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KAT14	ENST00000688188	c.-487C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 11		NM_001392073.1	ENSP00000508684.1
PET117	ENST00000432901.4	c.63C>T	p.Ala21Ala	synonymous_variant	Exon 1 of 2	1	NM_001164811.2	ENSP00000397881.2
KAT14	ENST00000688188	c.-487C>T		5_prime_UTR_variant	Exon 1 of 11		NM_001392073.1	ENSP00000508684.1

Frequencies

GnomAD3 genomes AF: 0.00397 AC: 604 AN: 151990 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.000700

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00308

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.00868

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00584

Gnomad OTH AF: 0.0105

GnomAD2 exomes AF: 0.00338 AC: 334 AN: 98744 AF XY: 0.00340

Gnomad AFR exome AF: 0.000404

Gnomad AMR exome AF: 0.00213

Gnomad ASJ exome AF: 0.000703

Gnomad EAS exome AF: 0.000213

Gnomad FIN exome AF: 0.00679

Gnomad NFE exome AF: 0.00520

Gnomad OTH exome AF: 0.00314

GnomAD4 exome AF: 0.00475 AC: 6392 AN: 1345900 Hom.: 22 Cov.: 29 AF XY: 0.00490 AC XY: 3254 AN XY: 663594

Gnomad4 AFR exome AF: 0.000759 AC: 21 AN: 27662

Gnomad4 AMR exome AF: 0.00290 AC: 89 AN: 30642

Gnomad4 ASJ exome AF: 0.000375 AC: 9 AN: 24030

Gnomad4 EAS exome AF: 0.000131 AC: 4 AN: 30552

Gnomad4 SAS exome AF: 0.00236 AC: 178 AN: 75448

Gnomad4 FIN exome AF: 0.00824 AC: 276 AN: 33506

Gnomad4 NFE exome AF: 0.00525 AC: 5573 AN: 1062252

Gnomad4 Remaining exome AF: 0.00386 AC: 217 AN: 56240

GnomAD4 genome AF: 0.00397 AC: 604 AN: 152100 Hom.: 2 Cov.: 32 AF XY: 0.00374 AC XY: 278 AN XY: 74382

Gnomad4 AFR AF: 0.000698 AC: 0.000698324 AN: 0.000698324

Gnomad4 AMR AF: 0.00308 AC: 0.00307511 AN: 0.00307511

Gnomad4 ASJ AF: 0.000288 AC: 0.000288018 AN: 0.000288018

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00228 AC: 0.00228027 AN: 0.00228027

Gnomad4 FIN AF: 0.00868 AC: 0.00867597 AN: 0.00867597

Gnomad4 NFE AF: 0.00584 AC: 0.00584425 AN: 0.00584425

Gnomad4 OTH AF: 0.0104 AC: 0.0104167 AN: 0.0104167

Alfa AF: 0.00343 Hom.: 0

Bravo AF: 0.00330

Asia WGS AF: 0.00173 AC: 6 AN: 3472

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PET117: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	12
DANN	Benign	0.93
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6
Mutation Taster		=99/1	polymorphism

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: rs184370918; hg19: chr20-18118662;