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rs7545236

Variant summary

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

The NM_000130.5(F5):c.374-66T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,416,802 control chromosomes in the GnomAD database, including 42,645 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.33 ( 10859 hom., cov: 32)
Exomes 𝑓: 0.20 ( 31786 hom. )

Consequence

F5
NM_000130.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.31
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 1-169560832-A-C is Benign according to our data. Variant chr1-169560832-A-C is described in ClinVar as [Benign]. Clinvar id is 1286244.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
F5NM_000130.5 linkuse as main transcriptc.374-66T>G intron_variant ENST00000367797.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
F5ENST00000367797.9 linkuse as main transcriptc.374-66T>G intron_variant 1 NM_000130.5 P2
F5ENST00000367796.3 linkuse as main transcriptc.374-66T>G intron_variant 5 A2

Frequencies

GnomAD3 genomes
AF:
0.326
AC:
49561
AN:
151802
Hom.:
10837
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.596
Gnomad AMI
AF:
0.0877
Gnomad AMR
AF:
0.294
Gnomad ASJ
AF:
0.205
Gnomad EAS
AF:
0.653
Gnomad SAS
AF:
0.194
Gnomad FIN
AF:
0.256
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.177
Gnomad OTH
AF:
0.300
GnomAD4 exome
AF:
0.197
AC:
248991
AN:
1264882
Hom.:
31786
AF XY:
0.195
AC XY:
124318
AN XY:
638590
show subpopulations
Gnomad4 AFR exome
AF:
0.597
Gnomad4 AMR exome
AF:
0.274
Gnomad4 ASJ exome
AF:
0.207
Gnomad4 EAS exome
AF:
0.596
Gnomad4 SAS exome
AF:
0.172
Gnomad4 FIN exome
AF:
0.256
Gnomad4 NFE exome
AF:
0.161
Gnomad4 OTH exome
AF:
0.240
GnomAD4 genome
AF:
0.327
AC:
49632
AN:
151920
Hom.:
10859
Cov.:
32
AF XY:
0.328
AC XY:
24397
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.597
Gnomad4 AMR
AF:
0.293
Gnomad4 ASJ
AF:
0.205
Gnomad4 EAS
AF:
0.652
Gnomad4 SAS
AF:
0.193
Gnomad4 FIN
AF:
0.256
Gnomad4 NFE
AF:
0.177
Gnomad4 OTH
AF:
0.307
Alfa
AF:
0.206
Hom.:
2245
Bravo
AF:
0.345
Asia WGS
AF:
0.451
AC:
1568
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 submitterclinical testingGeneDxNov 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
5.1
Dann
Benign
0.63

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.

Other links and lift over

dbSNP: rs7545236; hg19: chr1-169530070; API