rs11670728

Variant summary

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

The ENST00000593493.5(KLK2):​c.-282G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 533,426 control chromosomes in the GnomAD database, including 32,551 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 0.29 ( 7881 hom., cov: 25)
Exomes 𝑓: 0.34 ( 24670 hom. )

Consequence

KLK2
ENST00000593493.5 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.03
Variant links:
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]

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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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KLK2ENST00000596950.5 linkuse as main transcriptn.164G>A non_coding_transcript_exon_variant 2/41
KLK2ENST00000593493.5 linkuse as main transcriptc.-282G>A 5_prime_UTR_variant 2/43 ENSP00000472852
KLK2ENST00000595375.5 linkuse as main transcriptn.200G>A non_coding_transcript_exon_variant 2/34
KLK2ENST00000597509.5 linkuse as main transcriptn.294G>A non_coding_transcript_exon_variant 2/44

Frequencies

GnomAD3 genomes
AF:
0.294
AC:
43389
AN:
147648
Hom.:
7878
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.0932
Gnomad AMI
AF:
0.314
Gnomad AMR
AF:
0.403
Gnomad ASJ
AF:
0.282
Gnomad EAS
AF:
0.432
Gnomad SAS
AF:
0.183
Gnomad FIN
AF:
0.428
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.368
Gnomad OTH
AF:
0.273
GnomAD4 exome
AF:
0.344
AC:
132836
AN:
385660
Hom.:
24670
Cov.:
0
AF XY:
0.337
AC XY:
68025
AN XY:
201946
show subpopulations
Gnomad4 AFR exome
AF:
0.0910
Gnomad4 AMR exome
AF:
0.422
Gnomad4 ASJ exome
AF:
0.277
Gnomad4 EAS exome
AF:
0.440
Gnomad4 SAS exome
AF:
0.190
Gnomad4 FIN exome
AF:
0.429
Gnomad4 NFE exome
AF:
0.359
Gnomad4 OTH exome
AF:
0.324
GnomAD4 genome
AF:
0.294
AC:
43404
AN:
147766
Hom.:
7881
Cov.:
25
AF XY:
0.295
AC XY:
21141
AN XY:
71728
show subpopulations
Gnomad4 AFR
AF:
0.0931
Gnomad4 AMR
AF:
0.403
Gnomad4 ASJ
AF:
0.282
Gnomad4 EAS
AF:
0.432
Gnomad4 SAS
AF:
0.182
Gnomad4 FIN
AF:
0.428
Gnomad4 NFE
AF:
0.368
Gnomad4 OTH
AF:
0.278
Alfa
AF:
0.356
Hom.:
3744
Bravo
AF:
0.286
Asia WGS
AF:
0.303
AC:
1053
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
17
DANN
Benign
0.23

Splicing

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.

Other links and lift over

dbSNP: rs11670728; hg19: chr19-51376489; API