chr5-76716320-C-A

Variant names:

• chr5-76716320-C-A
• rs376593244
• NM_001992.5:c.13C>A

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4 BP7 BS2

The NM_001992.5(F2R):​c.13C>A​(p.Arg5Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000019 in 1,263,214 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.000019 (0 hom.)
• Consequence: F2R NM_001992.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540
• Publications: 3 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]

ENSG00000225407 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BP7: Synonymous conserved (PhyloP=0.54 with no splicing effect.
• BS2: High AC in GnomAdExome4 at 24 AD gene.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F2R	NM_001992.5	MANE Select	c.13C>A	p.Arg5Arg	synonymous	Exon 1 of 2	NP_001983.2	P25116
	F2R	NM_001311313.2		c.-473C>A		5_prime_UTR	Exon 1 of 3	NP_001298242.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F2R	ENST00000319211.5	TSL:1 MANE Select	c.13C>A	p.Arg5Arg	synonymous	Exon 1 of 2	ENSP00000321326.4	P25116
	F2R	ENST00000505600.1	TSL:2	c.13C>A	p.Arg5Arg	synonymous	Exon 1 of 2	ENSP00000426398.1	G3XAL6
	ENSG00000225407	ENST00000507514.1	TSL:3	n.-105G>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.0000190 AC: 24 AN: 1263214 Hom.: 0 Cov.: 31 AF XY: 0.0000196 AC XY: 12 AN XY: 613600

African (AFR) AF: 0.00 AC: 0 AN: 25604

American (AMR) AF: 0.00 AC: 0 AN: 19016

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20128

East Asian (EAS) AF: 0.00 AC: 0 AN: 28520

South Asian (SAS) AF: 0.00 AC: 0 AN: 61634

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31274

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4868

European-Non Finnish (NFE) AF: 0.0000216 AC: 22 AN: 1019576

Other (OTH) AF: 0.0000380 AC: 2 AN: 52594

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	15
DANN	Benign	0.93
PhyloP100		0.54
PromoterAI		-0.067	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.6

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: rs376593244; hg19: chr5-76012145;