19-16325536-CGGCTACGGCTGCGCCCCCG-C

Variant names:

• chr19-16325536-CGGCTACGGCTGCGCCCCCG-C
• NM_016270.4:c.401_419delACGGCTGCGCCCCCGGGCT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_016270.4(KLF2):​c.401_419delACGGCTGCGCCCCCGGGCT​(p.Tyr134fs) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as other (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KLF2 NM_016270.4 frameshift
• Clinical Significance: - - O:1
• Conservation: PhyloP100: 3.69

Genes affected

KLF2 (HGNC:6347): (KLF transcription factor 2) This gene encodes a protein that belongs to the Kruppel family of transcription factors. The encoded zinc finger protein is expressed early in mammalian development and is found in many different cell types. The protein acts to bind the CACCC box found in the promoter of target genes to activate their transcription. It plays a role in many processes during development and disease including adipogenesis, embryonic erythropoiesis, epithelial integrity, inflammation and t-cell viability. [provided by RefSeq, Mar 2017]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLF2	NM_016270.4	c.401_419delACGGCTGCGCCCCCGGGCT	p.Tyr134fs	frameshift_variant	Exon 2 of 3	ENST00000248071.6	NP_057354.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLF2	ENST00000248071.6	c.401_419delACGGCTGCGCCCCCGGGCT	p.Tyr134fs	frameshift_variant	Exon 2 of 3	1	NM_016270.4	ENSP00000248071.5
KLF2	ENST00000592003.1	c.75+543_75+561delACGGCTGCGCCCCCGGGCT		intron_variant	Intron 1 of 1	3		ENSP00000465035.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: -

Submissions summary: Other:1

Revision: -

Submissions by phenotype

Neoplasm Other:1

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: -

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-16436347;