rs550941932

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_005141.5(FGB):c.959-13_959-10delGTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 1,606,216 control chromosomes in the GnomAD database, including 23,864 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1851 hom., cov: 29)

Exomes 𝑓: 0.17 ( 22013 hom. )

Consequence

FGB
NM_005141.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 1.53

Variant links:

Genes affected

FGB (HGNC:3662): (fibrinogen beta chain) The protein encoded by this gene is the beta component of fibrinogen, a blood-borne glycoprotein comprised of three pairs of nonidentical polypeptide chains. Following vascular injury, fibrinogen is cleaved by thrombin to form fibrin which is the most abundant component of blood clots. In addition, various cleavage products of fibrinogen and fibrin regulate cell adhesion and spreading, display vasoconstrictor and chemotactic activities, and are mitogens for several cell types. Fibrinogen serves key roles in hemostasis and antimicrobial host defense. Mutations in this gene lead to several disorders, including afibrinogenemia, dysfibrinogenemia, hypodysfibrinogenemia and thrombotic tendency. [provided by RefSeq, Aug 2020]

FGB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 4-154569497-TTTTG-T is Benign according to our data. Variant chr4-154569497-TTTTG-T is described in ClinVar as [Benign]. Clinvar id is 259650.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-154569497-TTTTG-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGB	NM_005141.5 link	c.959-13_959-10delGTTT		intron_variant	Intron 6 of 7	ENST00000302068.9	NP_005132.2	P02675V9HVY1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FGB	ENST00000302068.9 link	c.959-16_959-13delTTTG	intron_variant	Intron 6 of 7	1	NM_005141.5	ENSP00000306099.4	P02675
FGB	ENST00000509493.1 link	c.302-16_302-13delTTTG	intron_variant	Intron 4 of 5	5		ENSP00000426757.1	D6REL8
FGB	ENST00000502545.5 link	n.939+191_939+194delTTTG	intron_variant	Intron 6 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21525

AN:

152020

Hom.:

1852

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0472

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.216

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.157

GnomAD3 exomes

AF:

0.164

AC:

39685

AN:

241336

Hom.:

3598

AF XY:

0.168

AC XY:

21990

AN XY:

131052

show subpopulations

Gnomad AFR exome

AF:

0.0448

Gnomad AMR exome

AF:

0.127

Gnomad ASJ exome

AF:

0.178

Gnomad EAS exome

AF:

0.224

Gnomad SAS exome

AF:

0.147

Gnomad FIN exome

AF:

0.166

Gnomad NFE exome

AF:

0.184

Gnomad OTH exome

AF:

0.191

GnomAD4 exome

AF:

0.170

AC:

247039

AN:

1454078

Hom.:

22013

AF XY:

0.171

AC XY:

123651

AN XY:

723020

show subpopulations

Gnomad4 AFR exome

AF:

0.0425

Gnomad4 AMR exome

AF:

0.130

Gnomad4 ASJ exome

AF:

0.178

Gnomad4 EAS exome

AF:

0.176

Gnomad4 SAS exome

AF:

0.154

Gnomad4 FIN exome

AF:

0.170

Gnomad4 NFE exome

AF:

0.176

Gnomad4 OTH exome

AF:

0.171

GnomAD4 genome

AF:

0.142

AC:

21529

AN:

152138

Hom.:

1851

Cov.:

AF XY:

0.140

AC XY:

10388

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.0471

Gnomad4 AMR

AF:

0.135

Gnomad4 ASJ

AF:

0.173

Gnomad4 EAS

AF:

0.216

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.167

Gnomad4 NFE

AF:

0.187

Gnomad4 OTH

AF:

0.155

Alfa

AF:

0.179

Hom.:

514

Bravo

AF:

0.139

Asia WGS

AF:

0.156

AC:

541

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Congenital afibrinogenemia

Benign:2

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Jun 10, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 01, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over