5-76717018-G-A

Variant names:

• chr5-76717018-G-A
• rs27135
• NM_001992.5:c.88+623G>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+623G>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 151,962 control chromosomes in the GnomAD database, including 15,630 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 (15630 hom., cov: 31)
• Consequence: F2R NM_001992.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 10 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 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+623G>A		intron	N/A	NP_001983.2
	F2R	NM_001311313.2		c.-398+623G>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+623G>A		intron	N/A	ENSP00000321326.4
	F2R	ENST00000505600.1	TSL:2	c.*254G>A		downstream_gene	N/A	ENSP00000426398.1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65799 AN: 151844 Hom.: 15627 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.433 AC: 65803 AN: 151962 Hom.: 15630 Cov.: 31 AF XY: 0.434 AC XY: 32209 AN XY: 74244

African (AFR) AF: 0.248 AC: 10285 AN: 41462

American (AMR) AF: 0.427 AC: 6521 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3468

East Asian (EAS) AF: 0.706 AC: 3641 AN: 5154

South Asian (SAS) AF: 0.298 AC: 1435 AN: 4818

European-Finnish (FIN) AF: 0.551 AC: 5801 AN: 10526

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35216 AN: 67942

Other (OTH) AF: 0.463 AC: 977 AN: 2108

Alfa AF: 0.492 Hom.: 72957

Bravo AF: 0.422

Asia WGS AF: 0.480 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.64
PhyloP100		0.14
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: rs27135; hg19: chr5-76012843;