rs6663533

chr1-169570110-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000130.5(F5):c.373+2111A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,100 control chromosomes in the GnomAD database, including 2,679 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (2679 hom., cov: 32)
• Consequence: F5 NM_000130.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F5	NM_000130.5	c.373+2111A>C		intron_variant		ENST00000367797.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F5	ENST00000367797.9	c.373+2111A>C		intron_variant		1	NM_000130.5	P2
F5	ENST00000367796.3	c.373+2111A>C		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19962 AN: 151982 Hom.: 2675 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0681

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0989

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.131 AC: 19969 AN: 152100 Hom.: 2679 Cov.: 32 AF XY: 0.123 AC XY: 9179 AN XY: 74374

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.0679

Gnomad4 ASJ AF: 0.0455

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0129

Gnomad4 FIN AF: 0.0232

Gnomad4 NFE AF: 0.0574

Gnomad4 OTH AF: 0.0979

Alfa AF: 0.0670 Hom.: 795

Bravo AF: 0.145

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.3
Dann	Benign	0.55

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

Other links and lift over

dbSNP: rs6663533; hg19: chr1-169539348;