19-51017229-GGA-AGC

Variant names:

• chr19-51017229-GGA-AGC
• NM_145888.3:c.148_150delTCCinsGCT
• KLK10 p.Ser50Ala

Variant summary

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

The NM_145888.3(KLK10):​c.148_150delTCCinsGCT​(p.Ser50Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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: 33)
• Consequence: KLK10 NM_145888.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 0 publications found

Genes affected

KLK10 (HGNC:6358): (kallikrein related peptidase 10) Kallikreins are a subgroup of serine proteases having diverse physiological functions. Growing evidence suggests that many kallikreins are implicated in carcinogenesis and some have potential as novel cancer and other disease biomarkers. This gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. Its encoded protein is secreted and may play a role in suppression of tumorigenesis in breast and prostate cancers. Alternate splicing of this gene results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145888.3. 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
	KLK10	NM_145888.3	MANE Select	c.148_150delTCCinsGCT	p.Ser50Ala	missense	N/A	NP_665895.1	O43240
	KLK10	NM_001077500.2		c.148_150delTCCinsGCT	p.Ser50Ala	missense	N/A	NP_001070968.1	O43240
	KLK10	NM_002776.5		c.148_150delTCCinsGCT	p.Ser50Ala	missense	N/A	NP_002767.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLK10	ENST00000358789.8	TSL:1 MANE Select	c.148_150delTCCinsGCT	p.Ser50Ala	missense	N/A	ENSP00000351640.2	O43240
	KLK10	ENST00000309958.7	TSL:1	c.148_150delTCCinsGCT	p.Ser50Ala	missense	N/A	ENSP00000311746.2	O43240
	KLK10	ENST00000601467.1	TSL:1	n.-145_-143delTCCinsGCT		non_coding_transcript_exon	Exon 2 of 5	ENSP00000472773.1	M0R2S4

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4

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: chr19-51520485;