rs58090485

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001286818.2(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 NM_001286818.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300

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

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0289

Gnomad4 AMR AF: 0.0502

Gnomad4 ASJ AF: 0.0513

Gnomad4 EAS AF: 0.0986

Gnomad4 SAS AF: 0.0783

Gnomad4 FIN AF: 0.0717

Gnomad4 NFE AF: 0.0771

Gnomad4 OTH AF: 0.0620

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58090485; hg19: chr13-73631518;