dbSNP rs2227356: F2RL3:c.*1973C>T (chr19-16892594-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003950.4(F2RL3):c.*1973C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 167,640 control chromosomes in the GnomAD database, including 6,458 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 0.26 ( 5967 hom., cov: 31)

Exomes 𝑓: 0.22 ( 491 hom. )

Consequence

F2RL3
NM_003950.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.58

Publications

6 publications found

Variant links:

Genes affected

F2RL3 (HGNC:3540): (F2R like thrombin or trypsin receptor 3) This gene encodes a member of the protease-activated receptor subfamily, part of the G-protein coupled receptor 1 family of proteins. The encoded receptor is proteolytically processed to reveal an extracellular N-terminal tethered ligand that binds to and activates the receptor. This receptor plays a role in blood coagulation, inflammation and response to pain. Hypomethylation at this gene may be associated with lung cancer in human patients. [provided by RefSeq, Sep 2016]

F2RL3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003950.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F2RL3	NM_003950.4	MANE Select	c.*1973C>T		3_prime_UTR	Exon 2 of 2	NP_003941.2	Q96RI0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F2RL3	ENST00000248076.4	TSL:1 MANE Select	c.*1973C>T		3_prime_UTR	Exon 2 of 2	ENSP00000248076.2	Q96RI0

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

38963

AN:

151808

Hom.:

5966

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0991

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.288

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.0629

Gnomad SAS

AF:

0.257

Gnomad FIN

AF:

0.358

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.339

Gnomad OTH

AF:

0.288

GnomAD4 exome

AF:

0.222

AC:

3495

AN:

15712

Hom.:

491

Cov.:

AF XY:

0.225

AC XY:

1879

AN XY:

8362

show subpopulations

African (AFR)

AF:

0.0641

AC:

AN:

640

American (AMR)

AF:

0.237

AC:

496

AN:

2092

Ashkenazi Jewish (ASJ)

AF:

0.248

AC:

AN:

294

East Asian (EAS)

AF:

0.0405

AC:

AN:

1258

South Asian (SAS)

AF:

0.198

AC:

331

AN:

1670

European-Finnish (FIN)

AF:

0.300

AC:

AN:

310

Middle Eastern (MID)

AF:

0.167

AC:

AN:

European-Non Finnish (NFE)

AF:

0.257

AC:

2212

AN:

8602

Other (OTH)

AF:

0.239

AC:

189

AN:

792

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

124

248

371

495

619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.257

AC:

38986

AN:

151928

Hom.:

5967

Cov.:

AF XY:

0.257

AC XY:

19067

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.0992

AC:

4112

AN:

41470

American (AMR)

AF:

0.288

AC:

4398

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.296

AC:

1027

AN:

3470

East Asian (EAS)

AF:

0.0633

AC:

327

AN:

5168

South Asian (SAS)

AF:

0.258

AC:

1243

AN:

4814

European-Finnish (FIN)

AF:

0.358

AC:

3763

AN:

10522

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.339

AC:

23046

AN:

67920

Other (OTH)

AF:

0.284

AC:

597

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1390

2780

4169

5559

6949

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.312

Hom.:

29642

Bravo

AF:

0.246

Asia WGS

AF:

0.166

AC:

579

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.24

(source)

DANN

Benign

0.61

PhyloP100

-1.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over