rs4253373
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000892.5(KLKB1):c.606C>A(p.His202Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000432 in 1,614,080 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000892.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLKB1 | NM_000892.5 | c.606C>A | p.His202Gln | missense_variant | 7/15 | ENST00000264690.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLKB1 | ENST00000264690.11 | c.606C>A | p.His202Gln | missense_variant | 7/15 | 1 | NM_000892.5 | P1 | |
KLKB1 | ENST00000511406.5 | n.636C>A | non_coding_transcript_exon_variant | 7/15 | 1 | ||||
KLKB1 | ENST00000513864.2 | c.492C>A | p.His164Gln | missense_variant | 8/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00242 AC: 369AN: 152206Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000672 AC: 169AN: 251484Hom.: 0 AF XY: 0.000449 AC XY: 61AN XY: 135918
GnomAD4 exome AF: 0.000225 AC: 329AN: 1461756Hom.: 2 Cov.: 33 AF XY: 0.000191 AC XY: 139AN XY: 727198
GnomAD4 genome ? AF: 0.00242 AC: 369AN: 152324Hom.: 2 Cov.: 33 AF XY: 0.00218 AC XY: 162AN XY: 74480
ClinVar
Submissions by phenotype
KLKB1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 15, 2019 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Oct 11, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at