chr3-58126713-A-G

Position:

chr3-58126713-A-G

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001457.4(FLNB):c.4173A>G(p.Ala1391=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 1,612,038 control chromosomes in the GnomAD database, including 366,694 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.73 ( 41517 hom., cov: 31)

Exomes 𝑓: 0.66 ( 325177 hom. )

Consequence

FLNB
NM_001457.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -0.252

Variant links:

Genes affected

FLNB (HGNC:3755): (filamin B) This gene encodes a member of the filamin family. The encoded protein interacts with glycoprotein Ib alpha as part of the process to repair vascular injuries. The platelet glycoprotein Ib complex includes glycoprotein Ib alpha, and it binds the actin cytoskeleton. Mutations in this gene have been found in several conditions: atelosteogenesis type 1 and type 3; boomerang dysplasia; autosomal dominant Larsen syndrome; and spondylocarpotarsal synostosis syndrome. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Nov 2009]

FLNB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 3-58126713-A-G is Benign according to our data. Variant chr3-58126713-A-G is described in ClinVar as [Benign]. Clinvar id is 258110.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-58126713-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.252 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
FLNB	NM_001457.4 linkuse as main transcript	c.4173A>G	p.Ala1391=	synonymous_variant	24/46	ENST00000295956.9	NP_001448.2
FLNB	NM_001164317.2 linkuse as main transcript	c.4173A>G	p.Ala1391=	synonymous_variant	24/47		NP_001157789.1
FLNB	NM_001164318.2 linkuse as main transcript	c.4173A>G	p.Ala1391=	synonymous_variant	24/46		NP_001157790.1
FLNB	NM_001164319.2 linkuse as main transcript	c.4173A>G	p.Ala1391=	synonymous_variant	24/45		NP_001157791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLNB	ENST00000295956.9 linkuse as main transcript	c.4173A>G	p.Ala1391=	synonymous_variant	24/46	1	NM_001457.4	ENSP00000295956	A1	O75369-1

Frequencies

GnomAD3 genomes

AF:

0.728

AC:

110523

AN:

151892

Hom.:

41454

Cov.:

show subpopulations

Gnomad AFR

AF:

0.894

Gnomad AMI

AF:

0.638

Gnomad AMR

AF:

0.719

Gnomad ASJ

AF:

0.659

Gnomad EAS

AF:

0.997

Gnomad SAS

AF:

0.781

Gnomad FIN

AF:

0.589

Gnomad MID

AF:

0.636

Gnomad NFE

AF:

0.631

Gnomad OTH

AF:

0.711

GnomAD3 exomes

AF:

0.707

AC:

177678

AN:

251412

Hom.:

64705

AF XY:

0.699

AC XY:

94962

AN XY:

135880

show subpopulations

Gnomad AFR exome

AF:

0.904

Gnomad AMR exome

AF:

0.774

Gnomad ASJ exome

AF:

0.661

Gnomad EAS exome

AF:

0.999

Gnomad SAS exome

AF:

0.755

Gnomad FIN exome

AF:

0.589

Gnomad NFE exome

AF:

0.626

Gnomad OTH exome

AF:

0.681

GnomAD4 exome

AF:

0.662

AC:

966804

AN:

1460028

Hom.:

325177

Cov.:

AF XY:

0.663

AC XY:

481759

AN XY:

726522

show subpopulations

Gnomad4 AFR exome

AF:

0.906

Gnomad4 AMR exome

AF:

0.768

Gnomad4 ASJ exome

AF:

0.660

Gnomad4 EAS exome

AF:

0.999

Gnomad4 SAS exome

AF:

0.751

Gnomad4 FIN exome

AF:

0.589

Gnomad4 NFE exome

AF:

0.633

Gnomad4 OTH exome

AF:

0.696

GnomAD4 genome

AF:

0.728

AC:

110645

AN:

152010

Hom.:

41517

Cov.:

AF XY:

0.731

AC XY:

54323

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.895

Gnomad4 AMR

AF:

0.720

Gnomad4 ASJ

AF:

0.659

Gnomad4 EAS

AF:

0.997

Gnomad4 SAS

AF:

0.780

Gnomad4 FIN

AF:

0.589

Gnomad4 NFE

AF:

0.631

Gnomad4 OTH

AF:

0.715

Alfa

AF:

0.672

Hom.:

24279

Bravo

AF:

0.746

EpiCase

AF:

0.640

EpiControl

AF:

0.637

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

FLNB-Related Spectrum Disorders

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

4.3

DANN

Benign

0.60

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

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

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