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GeneBe

rs2659058

Variant summary

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

The NM_002257.4(KLK1):c.46+853G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 979,162 control chromosomes in the GnomAD database, including 229,176 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 0.69 ( 36632 hom., cov: 30)
Exomes 𝑓: 0.68 ( 192544 hom. )

Consequence

KLK1
NM_002257.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.791
Variant links:
Genes affected
KLK1 (HGNC:6357): (kallikrein 1) 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. This protein is functionally conserved in its capacity to release the vasoactive peptide, Lys-bradykinin, from low molecular weight kininogen. [provided by RefSeq, Jul 2008]

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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=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KLK1NM_002257.4 linkuse as main transcriptc.46+853G>A intron_variant ENST00000301420.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KLK1ENST00000301420.3 linkuse as main transcriptc.46+853G>A intron_variant 1 NM_002257.4 P1P06870-1
KLK1ENST00000593325.5 linkuse as main transcriptc.122+27G>A intron_variant, NMD_transcript_variant 2
KLK1ENST00000593859.5 linkuse as main transcriptn.85+853G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.693
AC:
105135
AN:
151740
Hom.:
36582
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.701
Gnomad AMI
AF:
0.658
Gnomad AMR
AF:
0.741
Gnomad ASJ
AF:
0.633
Gnomad EAS
AF:
0.800
Gnomad SAS
AF:
0.633
Gnomad FIN
AF:
0.680
Gnomad MID
AF:
0.614
Gnomad NFE
AF:
0.679
Gnomad OTH
AF:
0.698
GnomAD3 exomes
AF:
0.669
AC:
119
AN:
178
Hom.:
40
AF XY:
0.615
AC XY:
32
AN XY:
52
show subpopulations
Gnomad AFR exome
AF:
0.684
Gnomad AMR exome
AF:
1.00
Gnomad ASJ exome
AF:
0.750
Gnomad EAS exome
AF:
0.667
Gnomad FIN exome
AF:
0.500
Gnomad NFE exome
AF:
0.676
Gnomad OTH exome
AF:
0.571
GnomAD4 exome
AF:
0.681
AC:
563722
AN:
827302
Hom.:
192544
Cov.:
17
AF XY:
0.682
AC XY:
260520
AN XY:
382264
show subpopulations
Gnomad4 AFR exome
AF:
0.687
Gnomad4 AMR exome
AF:
0.723
Gnomad4 ASJ exome
AF:
0.621
Gnomad4 EAS exome
AF:
0.791
Gnomad4 SAS exome
AF:
0.618
Gnomad4 FIN exome
AF:
0.698
Gnomad4 NFE exome
AF:
0.683
Gnomad4 OTH exome
AF:
0.670
GnomAD4 genome
AF:
0.693
AC:
105243
AN:
151860
Hom.:
36632
Cov.:
30
AF XY:
0.692
AC XY:
51336
AN XY:
74210
show subpopulations
Gnomad4 AFR
AF:
0.702
Gnomad4 AMR
AF:
0.742
Gnomad4 ASJ
AF:
0.633
Gnomad4 EAS
AF:
0.800
Gnomad4 SAS
AF:
0.633
Gnomad4 FIN
AF:
0.680
Gnomad4 NFE
AF:
0.679
Gnomad4 OTH
AF:
0.701
Alfa
AF:
0.678
Hom.:
4704
Bravo
AF:
0.702
Asia WGS
AF:
0.707
AC:
2457
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
5.0
Dann
Benign
0.50

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.

Other links and lift over

dbSNP: rs2659058; hg19: chr19-51326106; API