rs4253325
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM1BP6_Very_StrongBA1
The NM_000892.5(KLKB1):c.1679G>A(p.Arg560Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,601,918 control chromosomes in the GnomAD database, including 15,590 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLKB1 | NM_000892.5 | c.1679G>A | p.Arg560Gln | missense_variant | 14/15 | ENST00000264690.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLKB1 | ENST00000264690.11 | c.1679G>A | p.Arg560Gln | missense_variant | 14/15 | 1 | NM_000892.5 | P1 | |
KLKB1 | ENST00000511406.5 | n.1740G>A | non_coding_transcript_exon_variant | 14/15 | 1 | ||||
KLKB1 | ENST00000513864.2 | c.1472-702G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.162 AC: 24646AN: 151704Hom.: 2327 Cov.: 32
GnomAD3 exomes AF: 0.165 AC: 41154AN: 249108Hom.: 4163 AF XY: 0.161 AC XY: 21754AN XY: 134826
GnomAD4 exome AF: 0.123 AC: 178163AN: 1450098Hom.: 13264 Cov.: 29 AF XY: 0.125 AC XY: 89969AN XY: 721410
GnomAD4 genome ? AF: 0.162 AC: 24669AN: 151820Hom.: 2326 Cov.: 32 AF XY: 0.166 AC XY: 12310AN XY: 74202
ClinVar
Submissions by phenotype
KLKB1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 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
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | This variant is associated with the following publications: (PMID: 23413192, 25075649, 17318641, 32202057) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at