Variant rs10800456 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000367797.9(F5):c.1297-121T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 725,332 control chromosomes in the GnomAD database, including 71,226 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.44 ( 16103 hom., cov: 31)

Exomes 𝑓: 0.41 ( 55123 hom. )

Consequence

F5
ENST00000367797.9 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.467

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 1-169550860-A-G is Benign according to our data. Variant chr1-169550860-A-G is described in ClinVar as [Benign]. Clinvar id is 1268340.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
F5	NM_000130.5 linkuse as main transcript	c.1297-121T>C		intron_variant		ENST00000367797.9	NP_000121.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
F5	ENST00000367797.9 linkuse as main transcript	c.1297-121T>C		intron_variant		1	NM_000130.5	ENSP00000356771	P2
F5	ENST00000367796.3 linkuse as main transcript	c.1297-121T>C		intron_variant		5		ENSP00000356770	A2

Frequencies

GnomAD3 genomes

AF:

0.438

AC:

66531

AN:

151938

Hom.:

16059

Cov.:

show subpopulations

Gnomad AFR

AF:

0.547

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.530

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.895

Gnomad SAS

AF:

0.552

Gnomad FIN

AF:

0.432

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.322

Gnomad OTH

AF:

0.429

GnomAD4 exome

AF:

0.407

AC:

233162

AN:

573276

Hom.:

55123

AF XY:

0.408

AC XY:

125897

AN XY:

308200

show subpopulations

Gnomad4 AFR exome

AF:

0.537

Gnomad4 AMR exome

AF:

0.609

Gnomad4 ASJ exome

AF:

0.245

Gnomad4 EAS exome

AF:

0.908

Gnomad4 SAS exome

AF:

0.523

Gnomad4 FIN exome

AF:

0.424

Gnomad4 NFE exome

AF:

0.322

Gnomad4 OTH exome

AF:

0.403

GnomAD4 genome

AF:

0.438

AC:

66628

AN:

152056

Hom.:

16103

Cov.:

AF XY:

0.452

AC XY:

33629

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.548

Gnomad4 AMR

AF:

0.531

Gnomad4 ASJ

AF:

0.256

Gnomad4 EAS

AF:

0.895

Gnomad4 SAS

AF:

0.552

Gnomad4 FIN

AF:

0.432

Gnomad4 NFE

AF:

0.322

Gnomad4 OTH

AF:

0.434

Alfa

AF:

0.338

Hom.:

11026

Bravo

AF:

0.450

Asia WGS

AF:

0.720

AC:

2499

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

DANN

Benign

0.73

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