Variant chr5-76732339-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001992.5(F2R):c.114A>G(p.Leu38=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00293 in 1,605,272 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0027 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 45 hom. )

Consequence

F2R
NM_001992.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0490

Variant links:

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]

F2R links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 5-76732339-A-G is Benign according to our data. Variant chr5-76732339-A-G is described in ClinVar as [Benign]. Clinvar id is 714950.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.049 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00295 (4288/1452958) while in subpopulation MID AF= 0.0261 (149/5698). AF 95% confidence interval is 0.0227. There are 45 homozygotes in gnomad4_exome. There are 2153 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 414 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F2R	NM_001992.5 linkuse as main transcript	c.114A>G	p.Leu38=	synonymous_variant	2/2	ENST00000319211.5
F2R	NM_001311313.2 linkuse as main transcript	c.-250A>G		5_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F2R	ENST00000319211.5 linkuse as main transcript	c.114A>G	p.Leu38=	synonymous_variant	2/2	1	NM_001992.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00272

AC:

414

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000410

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00222

Gnomad ASJ

AF:

0.0418

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.00276

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00355

AC:

860

AN:

242302

Hom.:

AF XY:

0.00359

AC XY:

471

AN XY:

131126

show subpopulations

Gnomad AFR exome

AF:

0.000325

Gnomad AMR exome

AF:

0.00232

Gnomad ASJ exome

AF:

0.0347

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00164

Gnomad FIN exome

AF:

0.000418

Gnomad NFE exome

AF:

0.00319

Gnomad OTH exome

AF:

0.00649

GnomAD4 exome

AF:

0.00295

AC:

4288

AN:

1452958

Hom.:

Cov.:

AF XY:

0.00298

AC XY:

2153

AN XY:

721962

show subpopulations

Gnomad4 AFR exome

AF:

0.000636

Gnomad4 AMR exome

AF:

0.00250

Gnomad4 ASJ exome

AF:

0.0361

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00196

Gnomad4 FIN exome

AF:

0.000413

Gnomad4 NFE exome

AF:

0.00232

Gnomad4 OTH exome

AF:

0.00538

GnomAD4 genome

AF:

0.00272

AC:

414

AN:

152314

Hom.:

Cov.:

AF XY:

0.00281

AC XY:

209

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.000409

Gnomad4 AMR

AF:

0.00222

Gnomad4 ASJ

AF:

0.0418

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.00276

Gnomad4 OTH

AF:

0.00425

Alfa

AF:

0.00496

Hom.:

Bravo

AF:

0.00284

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.00436

EpiControl

AF:

0.00445

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.2

DANN

Benign

0.36

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over