Variant rs2075696 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145888.3(KLK10):c.679-14C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 1,607,592 control chromosomes in the GnomAD database, including 96,090 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.38 ( 11517 hom., cov: 31)

Exomes 𝑓: 0.34 ( 84573 hom. )

Consequence

KLK10
NM_145888.3 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.825

Variant links:

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]

KLK10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLK10	NM_145888.3 linkuse as main transcript	c.679-14C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000358789.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
KLK10	ENST00000358789.8 linkuse as main transcript	c.679-14C>T	splice_polypyrimidine_tract_variant, intron_variant	1	NM_145888.3	P1
KLK10	ENST00000309958.7 linkuse as main transcript	c.679-14C>T	splice_polypyrimidine_tract_variant, intron_variant	1		P1
KLK10	ENST00000601467.1 linkuse as main transcript	c.*255-14C>T	splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant	1
KLK10	ENST00000391805.5 linkuse as main transcript	c.679-14C>T	splice_polypyrimidine_tract_variant, intron_variant	5		P1

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

57475

AN:

151734

Hom.:

11504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.502

Gnomad AMI

AF:

0.361

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.258

Gnomad SAS

AF:

0.232

Gnomad FIN

AF:

0.263

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.336

Gnomad OTH

AF:

0.365

GnomAD3 exomes

AF:

0.344

AC:

84927

AN:

247178

Hom.:

15385

AF XY:

0.333

AC XY:

44527

AN XY:

133808

show subpopulations

Gnomad AFR exome

AF:

0.501

Gnomad AMR exome

AF:

0.477

Gnomad ASJ exome

AF:

0.271

Gnomad EAS exome

AF:

0.278

Gnomad SAS exome

AF:

0.248

Gnomad FIN exome

AF:

0.271

Gnomad NFE exome

AF:

0.338

Gnomad OTH exome

AF:

0.330

GnomAD4 exome

AF:

0.337

AC:

490013

AN:

1455740

Hom.:

84573

Cov.:

AF XY:

0.333

AC XY:

240863

AN XY:

724246

show subpopulations

Gnomad4 AFR exome

AF:

0.504

Gnomad4 AMR exome

AF:

0.471

Gnomad4 ASJ exome

AF:

0.271

Gnomad4 EAS exome

AF:

0.250

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.277

Gnomad4 NFE exome

AF:

0.341

Gnomad4 OTH exome

AF:

0.335

GnomAD4 genome

AF:

0.379

AC:

57527

AN:

151852

Hom.:

11517

Cov.:

AF XY:

0.373

AC XY:

27677

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.502

Gnomad4 AMR

AF:

0.431

Gnomad4 ASJ

AF:

0.276

Gnomad4 EAS

AF:

0.258

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.263

Gnomad4 NFE

AF:

0.336

Gnomad4 OTH

AF:

0.363

Alfa

AF:

0.346

Hom.:

2106

Bravo

AF:

0.401

Asia WGS

AF:

0.222

AC:

775

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.3

DANN

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over