Genetic Variant KLK3:p.Ala18Ala (chr19-50856247-A-G) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001648.2(KLK3):c.54A>G(p.Ala18Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 1,608,168 control chromosomes in the GnomAD database, including 137,079 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.37 ( 11211 hom., cov: 31)

Exomes 𝑓: 0.41 ( 125868 hom. )

Consequence

KLK3
NM_001648.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.44

Variant links:

Genes affected

KLK3 (HGNC:6364): (kallikrein related peptidase 3) 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. The gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. It encodes a single-chain glycoprotein, a protease which is synthesized in the epithelial cells of the prostate gland, and is present in seminal plasma. It is thought to function normally in the liquefaction of seminal coagulum, presumably by hydrolysis of the high molecular mass seminal vesicle protein. The serum level of this protein, called PSA in the clinical setting, is useful in the diagnosis and monitoring of prostatic carcinoma. Alternate splicing of this gene generates several transcript variants encoding different isoforms. [provided by RefSeq, Dec 2019]

KLK3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.06).

BP6

Variant 19-50856247-A-G is Benign according to our data. Variant chr19-50856247-A-G is described in ClinVar as [Benign]. Clinvar id is 3060459.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-2.44 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLK3	NM_001648.2 link	c.54A>G	p.Ala18Ala	synonymous_variant	Exon 2 of 5	ENST00000326003.7	NP_001639.1	P07288-1Q546G3
KLK3	NM_001030047.1 link	c.54A>G	p.Ala18Ala	synonymous_variant	Exon 2 of 5		NP_001025218.1	P07288-2
KLK3	NM_001030048.1 link	c.54A>G	p.Ala18Ala	synonymous_variant	Exon 2 of 5		NP_001025219.1	P07288-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLK3	ENST00000326003.7 link	c.54A>G	p.Ala18Ala	synonymous_variant	Exon 2 of 5	1	NM_001648.2	ENSP00000314151.1		P07288-1

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56149

AN:

151488

Hom.:

11206

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.444

Gnomad AMR

AF:

0.457

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.506

Gnomad SAS

AF:

0.227

Gnomad FIN

AF:

0.462

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.374

GnomAD3 exomes

AF:

0.403

AC:

100794

AN:

250044

Hom.:

21611

AF XY:

0.392

AC XY:

52913

AN XY:

135142

show subpopulations

Gnomad AFR exome

AF:

0.229

Gnomad AMR exome

AF:

0.524

Gnomad ASJ exome

AF:

0.385

Gnomad EAS exome

AF:

0.515

Gnomad SAS exome

AF:

0.233

Gnomad FIN exome

AF:

0.457

Gnomad NFE exome

AF:

0.411

Gnomad OTH exome

AF:

0.400

GnomAD4 exome

AF:

0.410

AC:

596503

AN:

1456562

Hom.:

125868

Cov.:

AF XY:

0.404

AC XY:

293048

AN XY:

724746

show subpopulations

Gnomad4 AFR exome

AF:

0.218

Gnomad4 AMR exome

AF:

0.511

Gnomad4 ASJ exome

AF:

0.387

Gnomad4 EAS exome

AF:

0.513

Gnomad4 SAS exome

AF:

0.238

Gnomad4 FIN exome

AF:

0.462

Gnomad4 NFE exome

AF:

0.420

Gnomad4 OTH exome

AF:

0.399

GnomAD4 genome

AF:

0.371

AC:

56174

AN:

151606

Hom.:

11211

Cov.:

AF XY:

0.371

AC XY:

27443

AN XY:

74064

show subpopulations

Gnomad4 AFR

AF:

0.229

Gnomad4 AMR

AF:

0.457

Gnomad4 ASJ

AF:

0.380

Gnomad4 EAS

AF:

0.506

Gnomad4 SAS

AF:

0.227

Gnomad4 FIN

AF:

0.462

Gnomad4 NFE

AF:

0.422

Gnomad4 OTH

AF:

0.380

Alfa

AF:

0.388

Hom.:

5082

Bravo

AF:

0.368

Asia WGS

AF:

0.363

AC:

1263

AN:

3478

EpiCase

AF:

0.407

EpiControl

AF:

0.407

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

KLK3-related disorder

Benign:1

Oct 18, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.016

DANN

Benign

0.20

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over