Variant chr19-51025641-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_144947.3(KLK11):c.87C>G(p.Pro29Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00558 in 1,587,434 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0044 ( 2 hom., cov: 31)

Exomes 𝑓: 0.0057 ( 33 hom. )

Consequence

KLK11
NM_144947.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.53

Variant links:

Genes affected

KLK11 (HGNC:6359): (kallikrein related peptidase 11) 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. Alternate splicing and the use of alternate promoters results in multiple transcript variants encoding distinct isoforms which are differentially expressed. [provided by RefSeq, Dec 2016]

KLK11 links:

KLK11 (HGNC:):

KLK11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 19-51025641-G-C is Benign according to our data. Variant chr19-51025641-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3387897.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-4.53 with no splicing effect.

BS2

High AC in GnomAd4 at 671 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLK11	NM_001136032.3 linkuse as main transcript	c.-10C>G		5_prime_UTR_variant	2/6	ENST00000453757.8	NP_001129504.1	Q9UBX7-1A0A1R3UDR5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLK11	ENST00000453757.8 linkuse as main transcript	c.-10C>G		5_prime_UTR_variant	2/6	1	NM_001136032.3	ENSP00000413958.2		Q9UBX7-1

Frequencies

GnomAD3 genomes

AF:

0.00441

AC:

671

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00130

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.00582

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.00273

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00619

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00367

AC:

783

AN:

213386

Hom.:

AF XY:

0.00377

AC XY:

435

AN XY:

115416

show subpopulations

Gnomad AFR exome

AF:

0.00107

Gnomad AMR exome

AF:

0.00155

Gnomad ASJ exome

AF:

0.00241

Gnomad EAS exome

AF:

0.000450

Gnomad SAS exome

AF:

0.000739

Gnomad FIN exome

AF:

0.00273

Gnomad NFE exome

AF:

0.00629

Gnomad OTH exome

AF:

0.00349

GnomAD4 exome

AF:

0.00570

AC:

8186

AN:

1435174

Hom.:

Cov.:

AF XY:

0.00551

AC XY:

3925

AN XY:

712192

show subpopulations

Gnomad4 AFR exome

AF:

0.000830

Gnomad4 AMR exome

AF:

0.00190

Gnomad4 ASJ exome

AF:

0.00322

Gnomad4 EAS exome

AF:

0.000318

Gnomad4 SAS exome

AF:

0.000831

Gnomad4 FIN exome

AF:

0.00323

Gnomad4 NFE exome

AF:

0.00680

Gnomad4 OTH exome

AF:

0.00466

GnomAD4 genome

AF:

0.00441

AC:

671

AN:

152260

Hom.:

Cov.:

AF XY:

0.00435

AC XY:

324

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.00130

Gnomad4 AMR

AF:

0.00582

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00269

Gnomad4 FIN

AF:

0.00273

Gnomad4 NFE

AF:

0.00619

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00223

Hom.:

Bravo

AF:

0.00450

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2024

KLK11: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.017

DANN

Benign

0.85

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over