rs253072

chr5-76728994-A-Gchr5-76728994-A-T

Variant summary

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

The NM_001992.5(F2R):c.89-3320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,990 control chromosomes in the GnomAD database, including 12,167 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 0.39 (12167 hom., cov: 32)
• Consequence: F2R NM_001992.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

F2R (HGNC:3537): (coagulation factor II thrombin receptor) Coagulation factor II receptor is a 7-transmembrane receptor involved in the regulation of thrombotic response. Proteolytic cleavage leads to the activation of the receptor. F2R is a G-protein coupled receptor family member. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F2R	NM_001992.5	c.89-3320A>G		intron_variant		ENST00000319211.5
F2R	NM_001311313.2	c.-276+161A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F2R	ENST00000319211.5	c.89-3320A>G		intron_variant		1	NM_001992.5	P1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59904 AN: 151872 Hom.: 12162 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.394 AC: 59935 AN: 151990 Hom.: 12167 Cov.: 32 AF XY: 0.393 AC XY: 29180 AN XY: 74326

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.393

Alfa AF: 0.395 Hom.: 8491

Bravo AF: 0.389

Asia WGS AF: 0.376 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.15

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: rs253072; hg19: chr5-76024819;