19-50876635-CTC-TTG

Variant names:

• chr19-50876635-CTC-TTG
• NM_005551.5:c.370_372delCTCinsTTG
• KLK2 p.125

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_005551.5(KLK2):​c.370_372delCTCinsTTG​(p.125) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KLK2 NM_005551.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.69
• Publications: 0 publications found

Genes affected

KLK2 (HGNC:6363): (kallikrein related peptidase 2) This gene encodes a member of the grandular kallikrein protein family. Kallikreins are a subgroup of serine proteases that are clustered on chromosome 19. Members of this family are involved in a diverse array of biological functions. The protein encoded by this gene is a highly active trypsin-like serine protease that selectively cleaves at arginine residues. This protein is primarily expressed in prostatic tissue and is responsible for cleaving pro-prostate-specific antigen into its enzymatically active form. This gene is highly expressed in prostate tumor cells and may be a prognostic maker for prostate cancer risk. Alternate splicing results in both coding and non-coding transcript variants. [provided by RefSeq, Jan 2012]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005551.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLK2	NM_005551.5	MANE Select	c.370_372delCTCinsTTG	p.125	synonymous	N/A	NP_005542.1	P20151-1
	KLK2	NM_001002231.3		c.370_372delCTCinsTTG	p.125	synonymous	N/A	NP_001002231.1	P20151-2
	KLK2	NM_001256080.2		c.64_66delCTCinsTTG	p.23	synonymous	N/A	NP_001243009.1	P20151-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLK2	ENST00000325321.8	TSL:1 MANE Select	c.370_372delCTCinsTTG	p.125	synonymous	N/A	ENSP00000313581.2	P20151-1
	KLK2	ENST00000358049.8	TSL:1	c.370_372delCTCinsTTG	p.125	synonymous	N/A	ENSP00000350748.3	P20151-2
	KLK2	ENST00000595316.5	TSL:1	n.*60_*62delCTCinsTTG		non_coding_transcript_exon	Exon 2 of 3	ENSP00000469770.1	Q6T774

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

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr19-51379891;