ClinVar Miner

Submissions for variant NM_000892.5(KLKB1):c.428G>A (p.Ser143Asn)

gnomAD frequency: 0.59489  dbSNP: rs3733402
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001723561 SCV001950725 benign not provided 2018-11-12 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 20981092, 24625756, 23251661, 17598838, 28508493, 28492530)
H3Africa Consortium RCV001528584 SCV002014641 benign not specified 2020-10-28 criteria provided, single submitter research While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.729, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error.
Breakthrough Genomics, Breakthrough Genomics RCV001723561 SCV005306633 benign not provided criteria provided, single submitter not provided
OMIM RCV000012817 SCV000033057 pathogenic Prekallikrein deficiency 2007-07-01 no assertion criteria provided literature only
Reproductive Health Research and Development, BGI Genomics RCV000012817 SCV001142341 benign Prekallikrein deficiency 2020-01-06 no assertion criteria provided curation NM_000892.3:c.428G>A (Ser143Asn) in the KLKB1 gene has an allele frequency of 0.738 in African subpopulation in the gnomAD database, including 43762 homozygous events. Ser143Asn was reported as N124S according to ClinVar's annotation. Katsuda et al reported three Japanese patients with plasma prekallikrein deficiency, who harbors homozygousity of Gly104Arg and Asn124Ser in 2007. Co-segregate analysis demonstrate the proband's parents were heterozygous of Gly104Arg Asn124-Ser\Gly104Arg+ (PMID: 17598838). Considering the high frequency of this variant, we classify the variant as benign. ACMG/AMP criteria applied: BA1, BS2.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV001528584 SCV001740539 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV001528584 SCV001932945 benign not specified no assertion criteria provided clinical testing

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