rs1054713
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_002257.4(KLK1):āc.405T>Cā(p.Asp135=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 1,613,394 control chromosomes in the GnomAD database, including 375,506 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: š 0.70 ( 37461 hom., cov: 30)
Exomes š: 0.68 ( 338045 hom. )
Consequence
KLK1
NM_002257.4 synonymous
NM_002257.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.10
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP7
?
Synonymous conserved (PhyloP=-5.1 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLK1 | NM_002257.4 | c.405T>C | p.Asp135= | synonymous_variant | 3/5 | ENST00000301420.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLK1 | ENST00000301420.3 | c.405T>C | p.Asp135= | synonymous_variant | 3/5 | 1 | NM_002257.4 | P1 | |
KLK1 | ENST00000593859.5 | n.444T>C | non_coding_transcript_exon_variant | 3/4 | 2 | ||||
KLK1 | ENST00000596300.1 | n.605T>C | non_coding_transcript_exon_variant | 1/3 | 2 | ||||
KLK1 | ENST00000593325.5 | c.*1214T>C | 3_prime_UTR_variant, NMD_transcript_variant | 4/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.700 AC: 106220AN: 151704Hom.: 37413 Cov.: 30
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GnomAD3 exomes AF: 0.696 AC: 174911AN: 251386Hom.: 61547 AF XY: 0.686 AC XY: 93248AN XY: 135858
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GnomAD4 exome AF: 0.678 AC: 991520AN: 1461572Hom.: 338045 Cov.: 54 AF XY: 0.676 AC XY: 491301AN XY: 727070
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GnomAD4 genome ? AF: 0.700 AC: 106326AN: 151822Hom.: 37461 Cov.: 30 AF XY: 0.698 AC XY: 51784AN XY: 74174
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at