chr5-76718494-G-A

Variant names:

• chr5-76718494-G-A
• rs37243
• NM_001992.5:c.88+2099G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001992.5(F2R):​c.88+2099G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,106 control chromosomes in the GnomAD database, including 15,637 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 0.43 (15637 hom., cov: 33)
• Consequence: F2R NM_001992.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001992.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F2R	NM_001992.5	MANE Select	c.88+2099G>A		intron	N/A	NP_001983.2
	F2R	NM_001311313.2		c.-398+2099G>A		intron	N/A	NP_001298242.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F2R	ENST00000319211.5	TSL:1 MANE Select	c.88+2099G>A		intron	N/A	ENSP00000321326.4

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65869 AN: 151988 Hom.: 15635 Cov.: 33

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.433 AC: 65872 AN: 152106 Hom.: 15637 Cov.: 33 AF XY: 0.434 AC XY: 32257 AN XY: 74362

African (AFR) AF: 0.251 AC: 10437 AN: 41522

American (AMR) AF: 0.422 AC: 6447 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1404 AN: 3472

East Asian (EAS) AF: 0.708 AC: 3657 AN: 5164

South Asian (SAS) AF: 0.293 AC: 1412 AN: 4824

European-Finnish (FIN) AF: 0.551 AC: 5831 AN: 10576

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35186 AN: 67944

Other (OTH) AF: 0.461 AC: 975 AN: 2114

Alfa AF: 0.464 Hom.: 2338

Bravo AF: 0.422

Asia WGS AF: 0.482 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.74
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs37243; hg19: chr5-76014319;