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GeneBe

5-76732741-T-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001992.5(F2R):c.516T>G(p.Ser172=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0052 in 1,614,234 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0054 ( 29 hom. )

Consequence

F2R
NM_001992.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.24
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-76732741-T-G is Benign according to our data. Variant chr5-76732741-T-G is described in ClinVar as [Benign]. Clinvar id is 781997.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-76732741-T-G is described in Lovd as [Likely_benign].
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.24 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 522 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
F2RNM_001992.5 linkuse as main transcriptc.516T>G p.Ser172= synonymous_variant 2/2 ENST00000319211.5
F2RNM_001311313.2 linkuse as main transcriptc.153T>G p.Ser51= synonymous_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
F2RENST00000319211.5 linkuse as main transcriptc.516T>G p.Ser172= synonymous_variant 2/21 NM_001992.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00343
AC:
522
AN:
152224
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00142
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000982
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000620
Gnomad FIN
AF:
0.00367
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00588
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00342
AC:
859
AN:
251486
Hom.:
2
AF XY:
0.00341
AC XY:
463
AN XY:
135912
show subpopulations
Gnomad AFR exome
AF:
0.00129
Gnomad AMR exome
AF:
0.000954
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00108
Gnomad FIN exome
AF:
0.00360
Gnomad NFE exome
AF:
0.00590
Gnomad OTH exome
AF:
0.00375
GnomAD4 exome
AF:
0.00539
AC:
7880
AN:
1461892
Hom.:
29
Cov.:
32
AF XY:
0.00526
AC XY:
3825
AN XY:
727246
show subpopulations
Gnomad4 AFR exome
AF:
0.000777
Gnomad4 AMR exome
AF:
0.00123
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000974
Gnomad4 FIN exome
AF:
0.00404
Gnomad4 NFE exome
AF:
0.00651
Gnomad4 OTH exome
AF:
0.00424
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00343
AC:
522
AN:
152342
Hom.:
1
Cov.:
32
AF XY:
0.00328
AC XY:
244
AN XY:
74502
show subpopulations
Gnomad4 AFR
AF:
0.00142
Gnomad4 AMR
AF:
0.000981
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000621
Gnomad4 FIN
AF:
0.00367
Gnomad4 NFE
AF:
0.00588
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00502
Hom.:
2
Bravo
AF:
0.00302
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00551
EpiControl
AF:
0.00409

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
Cadd
Benign
0.24
Dann
Benign
0.60

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.

Other links and lift over

dbSNP: rs5894; hg19: chr5-76028566; COSMIC: COSV100058737; API