4-154586438-T-C

Position:

chr4-154586438-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_021871.4(FGA):c.991A>G(p.Thr331Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 1,613,298 control chromosomes in the GnomAD database, including 60,604 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.29 ( 6817 hom., cov: 31)

Exomes 𝑓: 0.27 ( 53787 hom. )

Consequence

FGA
NM_021871.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:6O:1

Conservation

PhyloP100: -7.95

Variant links:

Genes affected

FGA (HGNC:3661): (fibrinogen alpha chain) This gene encodes the alpha subunit of the coagulation factor fibrinogen, which is a component of the blood clot. Following vascular injury, the encoded preproprotein is proteolytically processed by thrombin during the conversion of fibrinogen to fibrin. Mutations in this gene lead to several disorders, including dysfibrinogenemia, hypofibrinogenemia, afibrinogenemia and renal amyloidosis. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that undergoes proteolytic processing. [provided by RefSeq, Jan 2016]

FGA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=3.001392E-4).

BP6

Variant 4-154586438-T-C is Benign according to our data. Variant chr4-154586438-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 16420.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=4}. Variant chr4-154586438-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGA	NM_021871.4 linkuse as main transcript	c.991A>G	p.Thr331Ala	missense_variant	5/5	ENST00000403106.8	NP_068657.1	P02671-2
FGA	NM_000508.5 linkuse as main transcript	c.991A>G	p.Thr331Ala	missense_variant	5/6		NP_000499.1	P02671-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGA	ENST00000403106.8 linkuse as main transcript	c.991A>G	p.Thr331Ala	missense_variant	5/5	1	NM_021871.4	ENSP00000385981.3		P02671-2
FGA	ENST00000651975.2 linkuse as main transcript	c.991A>G	p.Thr331Ala	missense_variant	5/6			ENSP00000498441.1		P02671-1

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44526

AN:

151580

Hom.:

6806

Cov.:

show subpopulations

Gnomad AFR

AF:

0.363

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.248

Gnomad ASJ

AF:

0.182

Gnomad EAS

AF:

0.445

Gnomad SAS

AF:

0.303

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.260

GnomAD3 exomes

AF:

0.286

AC:

71751

AN:

251264

Hom.:

10915

AF XY:

0.285

AC XY:

38679

AN XY:

135786

show subpopulations

Gnomad AFR exome

AF:

0.369

Gnomad AMR exome

AF:

0.244

Gnomad ASJ exome

AF:

0.186

Gnomad EAS exome

AF:

0.455

Gnomad SAS exome

AF:

0.320

Gnomad FIN exome

AF:

0.318

Gnomad NFE exome

AF:

0.254

Gnomad OTH exome

AF:

0.251

GnomAD4 exome

AF:

0.266

AC:

388747

AN:

1461600

Hom.:

53787

Cov.:

AF XY:

0.267

AC XY:

194139

AN XY:

727100

show subpopulations

Gnomad4 AFR exome

AF:

0.363

Gnomad4 AMR exome

AF:

0.242

Gnomad4 ASJ exome

AF:

0.186

Gnomad4 EAS exome

AF:

0.467

Gnomad4 SAS exome

AF:

0.327

Gnomad4 FIN exome

AF:

0.315

Gnomad4 NFE exome

AF:

0.253

Gnomad4 OTH exome

AF:

0.255

GnomAD4 genome

AF:

0.294

AC:

44567

AN:

151698

Hom.:

6817

Cov.:

AF XY:

0.295

AC XY:

21846

AN XY:

74128

show subpopulations

Gnomad4 AFR

AF:

0.363

Gnomad4 AMR

AF:

0.248

Gnomad4 ASJ

AF:

0.182

Gnomad4 EAS

AF:

0.445

Gnomad4 SAS

AF:

0.304

Gnomad4 FIN

AF:

0.312

Gnomad4 NFE

AF:

0.254

Gnomad4 OTH

AF:

0.258

Alfa

AF:

0.260

Hom.:

2420

Bravo

AF:

0.293

TwinsUK

AF:

0.252

AC:

934

ALSPAC

AF:

0.257

AC:

989

ESP6500AA

AF:

0.364

AC:

1603

ESP6500EA

AF:

0.252

AC:

2168

ExAC

AF:

0.287

AC:

34860

Asia WGS

AF:

0.326

AC:

1129

AN:

3478

EpiCase

AF:

0.242

EpiControl

AF:

0.247

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:6Other:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not specified

Benign:3

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, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

not provided

Uncertain:1Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Apr 23, 2019	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	This variant is associated with the following publications: (PMID: 32853977, 26139837, 18057060, 24821635, 10318664, 17433418, 19652888, 23894515, 19143925, 22353194, 10910940) -

Congenital afibrinogenemia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Mar 06, 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. -

Familial visceral amyloidosis, Ostertag type

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Mar 06, 2018

Venous thromboembolism, susceptibility to

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Mar 01, 2006

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.62

CADD

Benign

0.0030

DANN

Benign

0.60

DEOGEN2

Benign

0.20

T;.

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.0070

LIST_S2

Benign

0.48

T;T

MetaRNN

Benign

0.00030

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.12

N;N

PrimateAI

Benign

0.27

PROVEAN

Benign

-1.1

N;N

REVEL

Benign

0.092

Sift

Benign

0.47

T;T

Sift4G

Benign

0.83

T;T

Polyphen

0.025

B;B

Vest4

0.017

MPC

0.058

ClinPred

0.0091

GERP RS

-6.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.021

gMVP

0.18

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