chr5-76734971-T-C

Position:

• chr5-76734971-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	UniProt
F2R	NM_001992.5	c.*1468T>C		3_prime_UTR_variant	2/2	ENST00000319211.5
F2R	NM_001311313.2	c.*1468T>C		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F2R	ENST00000319211.5	c.*1468T>C		3_prime_UTR_variant	2/2	1	NM_001992.5	P1

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

Gnomad4 EAS exome AF: 0.239

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

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0845

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.228

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

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: rs1801719; hg19: chr5-76030796;