5-76734971-T-C

Variant names:

• chr5-76734971-T-C
• rs1801719
• NM_001992.5:c.*1468T>C

Variant summary

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

The NM_001992.5(F2R):​c.*1468T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,208 control chromosomes in the GnomAD database, including 4,302 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 0.23 (4300 hom., cov: 32)
  • Exomes 𝑓: 0.24 (2 hom.)
• Consequence: F2R NM_001992.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670
• Publications: 7 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=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
F2R	NM_001992.5	c.*1468T>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000319211.5	NP_001983.2
F2R	NM_001311313.2	c.*1468T>C		3_prime_UTR_variant	Exon 3 of 3		NP_001298242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
F2R	ENST00000319211.5	c.*1468T>C		3_prime_UTR_variant	Exon 2 of 2	1	NM_001992.5	ENSP00000321326.4

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35278 AN: 151952 Hom.: 4295 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0845

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.226

GnomAD4 exome AF: 0.239 AC: 33 AN: 138 Hom.: 2 Cov.: 0 AF XY: 0.237 AC XY: 18 AN XY: 76

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.239 AC: 33 AN: 138

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.232 AC: 35297 AN: 152070 Hom.: 4300 Cov.: 32 AF XY: 0.230 AC XY: 17090 AN XY: 74342

African (AFR) AF: 0.202 AC: 8386 AN: 41494

American (AMR) AF: 0.182 AC: 2782 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3470

East Asian (EAS) AF: 0.0845 AC: 438 AN: 5184

South Asian (SAS) AF: 0.140 AC: 674 AN: 4826

European-Finnish (FIN) AF: 0.289 AC: 3053 AN: 10554

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18616 AN: 67964

Other (OTH) AF: 0.228 AC: 481 AN: 2110

Alfa AF: 0.254 Hom.: 1019

Bravo AF: 0.220

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.87
PhyloP100		0.67
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: rs1801719; hg19: chr5-76030796;