20-18166059-A-G

Variant names:

• chr20-18166059-A-G
• rs1205200
• NM_001392073.1:c.1668+3114A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001392073.1(KAT14):​c.1668+3114A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,092 control chromosomes in the GnomAD database, including 4,274 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 (4274 hom., cov: 32)
• Consequence: KAT14 NM_001392073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 1 publications found

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]

KAT14 Gene-Disease associations (from GenCC):

• multiple congenital anomalies/dysmorphic syndrome

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KAT14	NM_001392073.1	c.1668+3114A>G		intron_variant	Intron 7 of 10	ENST00000688188.1	NP_001379002.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KAT14	ENST00000688188.1	c.1668+3114A>G		intron_variant	Intron 7 of 10		NM_001392073.1	ENSP00000508684.1

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34540 AN: 151974 Hom.: 4272 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.193

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.227 AC: 34553 AN: 152092 Hom.: 4274 Cov.: 32 AF XY: 0.232 AC XY: 17258 AN XY: 74364

African (AFR) AF: 0.222 AC: 9204 AN: 41500

American (AMR) AF: 0.241 AC: 3687 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3468

East Asian (EAS) AF: 0.513 AC: 2647 AN: 5162

South Asian (SAS) AF: 0.325 AC: 1562 AN: 4810

European-Finnish (FIN) AF: 0.232 AC: 2454 AN: 10572

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13939 AN: 67982

Other (OTH) AF: 0.192 AC: 404 AN: 2106

Alfa AF: 0.203 Hom.: 6458

Bravo AF: 0.227

Asia WGS AF: 0.392 AC: 1362 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	3.8
DANN	Benign	0.57
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1205200; hg19: chr20-18146703;