rs58090485

Variant names:

• chr13-73057380-GA-G
• rs58090485
• ENST00000539231.5:c.-13+2223delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000539231.5(KLF5):​c.-13+2223delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0607 in 152,266 control chromosomes in the GnomAD database, including 350 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.061 (350 hom., cov: 32)
• Consequence: KLF5 ENST00000539231.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• Publications: 2 publications found

Genes affected

KLF5 (HGNC:6349): (KLF transcription factor 5) This gene encodes a member of the Kruppel-like factor subfamily of zinc finger proteins. The encoded protein is a transcriptional activator that binds directly to a specific recognition motif in the promoters of target genes. This protein acts downstream of multiple different signaling pathways and is regulated by post-translational modification. It may participate in both promoting and suppressing cell proliferation. Expression of this gene may be changed in a variety of different cancers and in cardiovascular disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

ACMG classification

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

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLF5	NM_001286818.2	c.-13+2223delA		intron_variant	Intron 1 of 3		NP_001273747.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLF5	ENST00000539231.5	c.-13+2223delA		intron_variant	Intron 1 of 3	1		ENSP00000440407.1
KLF5	ENST00000477333.5	n.183+2223delA		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9246 AN: 152148 Hom.: 350 Cov.: 32

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0502

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0607 AC: 9250 AN: 152266 Hom.: 350 Cov.: 32 AF XY: 0.0607 AC XY: 4519 AN XY: 74448

African (AFR) AF: 0.0289 AC: 1199 AN: 41558

American (AMR) AF: 0.0502 AC: 768 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3472

East Asian (EAS) AF: 0.0986 AC: 511 AN: 5180

South Asian (SAS) AF: 0.0783 AC: 378 AN: 4830

European-Finnish (FIN) AF: 0.0717 AC: 759 AN: 10588

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0771 AC: 5247 AN: 68012

Other (OTH) AF: 0.0620 AC: 131 AN: 2114

Alfa AF: 0.0188 Hom.: 13

Bravo AF: 0.0575

Asia WGS AF: 0.0620 AC: 213 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.30
Mutation Taster		=95/5	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs58090485; hg19: chr13-73631518;