1-197040378-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PP3_Moderate BP6_Moderate BA1

The NM_001994.3(F13B):c.1952+144C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 622,928 control chromosomes in the GnomAD database, including 20,004 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.18 (3843 hom., cov: 32)
  • Exomes 𝑓: 0.22 (16161 hom.)
• Consequence: F13B NM_001994.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0480

Genes affected

F13B (HGNC:3534): (coagulation factor XIII B chain) This gene encodes coagulation factor XIII B subunit. Coagulation factor XIII is the last zymogen to become activated in the blood coagulation cascade. Plasma factor XIII is a heterotetramer composed of 2 A subunits and 2 B subunits. The A subunits have catalytic function, and the B subunits do not have enzymatic activity and may serve as a plasma carrier molecules. Platelet factor XIII is comprised only of 2 A subunits, which are identical to those of plasma origin. Upon activation by the cleavage of the activation peptide by thrombin and in the presence of calcium ion, the plasma factor XIII dissociates its B subunits and yields the same active enzyme, factor XIIIa, as platelet factor XIII. This enzyme acts as a transglutaminase to catalyze the formation of gamma-glutamyl-epsilon-lysine crosslinking between fibrin molecules, thus stabilizing the fibrin clot. Factor XIII deficiency is classified into two categories: type I deficiency, characterized by the lack of both the A and B subunits; and type II deficiency, characterized by the lack of the A subunit alone. These defects can result in a lifelong bleeding tendency, defective wound healing, and habitual abortion. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• BP6: Variant 1-197040378-G-C is Benign according to our data. Variant chr1-197040378-G-C is described in ClinVar as [Benign]. Clinvar id is 1245718.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F13B	NM_001994.3	c.1952+144C>G		intron_variant		ENST00000367412.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F13B	ENST00000367412.2	c.1952+144C>G		intron_variant		1	NM_001994.3	P1
F13B	ENST00000649282.1	c.707+144C>G		intron_variant
F13B	ENST00000490002.1	n.364-1C>G		splice_acceptor_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26643 AN: 151442 Hom.: 3835 Cov.: 32

Gnomad AFR AF: 0.0441

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.190

GnomAD4 exome AF: 0.218 AC: 102610 AN: 471374 Hom.: 16161 Cov.: 5 AF XY: 0.219 AC XY: 55329 AN XY: 252236

Gnomad4 AFR exome AF: 0.0407

Gnomad4 AMR exome AF: 0.400

Gnomad4 ASJ exome AF: 0.176

Gnomad4 EAS exome AF: 0.678

Gnomad4 SAS exome AF: 0.279

Gnomad4 FIN exome AF: 0.240

Gnomad4 NFE exome AF: 0.157

Gnomad4 OTH exome AF: 0.212

GnomAD4 genome AF: 0.176 AC: 26654 AN: 151554 Hom.: 3843 Cov.: 32 AF XY: 0.188 AC XY: 13940 AN XY: 74038

Gnomad4 AFR AF: 0.0440

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.190

Alfa AF: 0.159 Hom.: 299

Bravo AF: 0.179

Asia WGS AF: 0.476 AC: 1649 AN: 3466

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

This variant is associated with the following publications: (PMID: 28865246, 27821352, 18716611) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Pathogenic	26
Dann	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.99		Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12134960; hg19: chr1-197009508;