1-169542317-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000130.5(F5):c.2773A>G(p.Lys925Glu) 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 1,613,780 control chromosomes in the GnomAD database, including 60,109 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 4743 hom., cov: 31)

Exomes 𝑓: 0.27 ( 55366 hom. )

Consequence

F5
NM_000130.5 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: -0.376

Publications

45 publications found

Variant links:

Genes affected

F5 (HGNC:3542): (coagulation factor V) This gene encodes an essential cofactor of the blood coagulation cascade. This factor circulates in plasma, and is converted to the active form by the release of the activation peptide by thrombin during coagulation. This generates a heavy chain and a light chain which are held together by calcium ions. The activated protein is a cofactor that participates with activated coagulation factor X to activate prothrombin to thrombin. Defects in this gene result in either an autosomal recessive hemorrhagic diathesis or an autosomal dominant form of thrombophilia, which is known as activated protein C resistance. [provided by RefSeq, Oct 2008]

F5 Gene-Disease associations (from GenCC):

thrombophilia due to activated protein C resistance
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
congenital factor V deficiency
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, Labcorp Genetics (formerly Invitae)
East Texas bleeding disorder
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

F5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0026506782).

BP6

Variant 1-169542317-T-C is Benign according to our data. Variant chr1-169542317-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 255202.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
F5	NM_000130.5 link	c.2773A>G	p.Lys925Glu	missense_variant	Exon 13 of 25	ENST00000367797.9	NP_000121.2	P12259

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
F5	ENST00000367797.9 link	c.2773A>G	p.Lys925Glu	missense_variant	Exon 13 of 25	1	NM_000130.5	ENSP00000356771.3		P12259
F5	ENST00000367796.3 link	c.2788A>G	p.Lys930Glu	missense_variant	Exon 13 of 25	5		ENSP00000356770.3		A0A0A0MRJ7

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37254

AN:

151954

Hom.:

4731

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.341

Gnomad ASJ

AF:

0.168

Gnomad EAS

AF:

0.234

Gnomad SAS

AF:

0.323

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.242

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.261

GnomAD2 exomes

AF:

0.279

AC:

69910

AN:

251014

AF XY:

0.278

show subpopulations

Gnomad AFR exome

AF:

0.179

Gnomad AMR exome

AF:

0.415

Gnomad ASJ exome

AF:

0.177

Gnomad EAS exome

AF:

0.221

Gnomad FIN exome

AF:

0.213

Gnomad NFE exome

AF:

0.268

Gnomad OTH exome

AF:

0.285

GnomAD4 exome

AF:

0.272

AC:

397264

AN:

1461708

Hom.:

55366

Cov.:

AF XY:

0.273

AC XY:

198289

AN XY:

727160

show subpopulations

African (AFR)

AF:

0.180

AC:

6014

AN:

33474

American (AMR)

AF:

0.409

AC:

18273

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.176

AC:

4594

AN:

26136

East Asian (EAS)

AF:

0.226

AC:

8990

AN:

39698

South Asian (SAS)

AF:

0.325

AC:

28070

AN:

86250

European-Finnish (FIN)

AF:

0.217

AC:

11597

AN:

53414

Middle Eastern (MID)

AF:

0.273

AC:

1575

AN:

5768

European-Non Finnish (NFE)

AF:

0.272

AC:

302218

AN:

1111866

Other (OTH)

AF:

0.264

AC:

15933

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

19308

38616

57925

77233

96541

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.245

AC:

37295

AN:

152072

Hom.:

4743

Cov.:

AF XY:

0.247

AC XY:

18356

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.183

AC:

7590

AN:

41492

American (AMR)

AF:

0.342

AC:

5212

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.168

AC:

581

AN:

3466

East Asian (EAS)

AF:

0.234

AC:

1211

AN:

5172

South Asian (SAS)

AF:

0.323

AC:

1559

AN:

4820

European-Finnish (FIN)

AF:

0.211

AC:

2241

AN:

10602

Middle Eastern (MID)

AF:

0.233

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.267

AC:

18110

AN:

67950

Other (OTH)

AF:

0.260

AC:

549

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1452

2904

4355

5807

7259

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.262

Hom.:

13007

Bravo

AF:

0.254

TwinsUK

AF:

0.270

AC:

1000

ALSPAC

AF:

0.280

AC:

1080

ESP6500AA

AF:

0.184

AC:

812

ESP6500EA

AF:

0.274

AC:

2355

ExAC

AF:

0.274

AC:

33213

Asia WGS

AF:

0.283

AC:

983

AN:

3478

EpiCase

AF:

0.269

EpiControl

AF:

0.270

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

not provided

Benign:2

Nov 11, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Thrombophilia due to activated protein C resistance

Benign:2

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Congenital factor V deficiency

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Budd-Chiari syndrome

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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. -

Factor V deficiency

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Thrombophilia due to thrombin defect

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.88

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.062

(source)

DANN

Benign

0.24

DEOGEN2

Benign

0.013

T;T

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.00071

LIST_S2

Benign

0.25

T;T

MetaRNN

Benign

0.0027

T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

-0.51

N;.

PhyloP100

-0.38

PrimateAI

Benign

0.46

PROVEAN

Benign

0.42

N;N

REVEL

Benign

0.077

Sift

Benign

1.0

T;T

Sift4G

Benign

0.99

T;T

Polyphen

0.0

B;.

Vest4

0.038

MPC

0.12

ClinPred

0.0040

GERP RS

-5.1

Varity_R

0.040

gMVP

0.19

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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1-169542317-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over