NM_000892.5:c.59-954A>T

Variant names:

• chr4-186231173-A-T
• rs4241816
• NM_000892.5:c.59-954A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000892.5(KLKB1):​c.59-954A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,950 control chromosomes in the GnomAD database, including 24,265 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 0.56 (24265 hom., cov: 32)
• Consequence: KLKB1 NM_000892.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 17 publications found

Genes affected

KLKB1 (HGNC:6371): (kallikrein B1) This gene encodes a glycoprotein that participates in the surface-dependent activation of blood coagulation, fibrinolysis, kinin generation and inflammation. The encoded preproprotein present in plasma as a non-covalent complex with high molecular weight kininogen undergoes proteolytic processing mediated by activated coagulation factor XII to generate a disulfide-linked, heterodimeric serine protease comprised of heavy and light chains. Certain mutations in this gene cause prekallikrein deficiency. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

KLKB1 Gene-Disease associations (from GenCC):

• inherited prekallikrein deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, Labcorp Genetics (formerly Invitae)

ENSG00000290316 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000892.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLKB1	NM_000892.5	MANE Select	c.59-954A>T		intron	N/A	NP_000883.2
	KLKB1	NM_001440521.1		c.59-954A>T		intron	N/A	NP_001427450.1
	KLKB1	NM_001318394.2		c.-56-954A>T		intron	N/A	NP_001305323.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLKB1	ENST00000264690.11	TSL:1 MANE Select	c.59-954A>T		intron	N/A	ENSP00000264690.6
	ENSG00000290316	ENST00000511608.5	TSL:5	c.200-954A>T		intron	N/A	ENSP00000426629.1
	KLKB1	ENST00000511406.5	TSL:1	n.89-954A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85134 AN: 151832 Hom.: 24234 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.554

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.561 AC: 85217 AN: 151950 Hom.: 24265 Cov.: 32 AF XY: 0.561 AC XY: 41650 AN XY: 74284

African (AFR) AF: 0.645 AC: 26717 AN: 41410

American (AMR) AF: 0.577 AC: 8811 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1539 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3493 AN: 5136

South Asian (SAS) AF: 0.399 AC: 1924 AN: 4828

European-Finnish (FIN) AF: 0.582 AC: 6141 AN: 10554

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.511 AC: 34710 AN: 67960

Other (OTH) AF: 0.555 AC: 1173 AN: 2112

Alfa AF: 0.540 Hom.: 2807

Bravo AF: 0.570

Asia WGS AF: 0.526 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.73
PhyloP100		0.065
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4241816; hg19: chr4-187152327;