Variant 19-35450346-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001370087.1(FFAR2):c.632T>A(p.Leu211His) variant causes a missense change. The variant allele was found at a frequency of 0.0717 in 1,614,116 control chromosomes in the GnomAD database, including 4,781 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.055 ( 296 hom., cov: 32)

Exomes 𝑓: 0.074 ( 4485 hom. )

Consequence

FFAR2
NM_001370087.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.38

Variant links:

Genes affected

FFAR2 (HGNC:4501): (free fatty acid receptor 2) This gene encodes a member of the GP40 family of G protein-coupled receptors that are clustered together on chromosome 19. The encoded protein is a receptor for short chain free fatty acids and may be involved in the inflammatory response and in regulating lipid plasma levels. [provided by RefSeq, Apr 2009]

FFAR2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001258254).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FFAR2	NM_001370087.1 linkuse as main transcript	c.632T>A	p.Leu211His	missense_variant	2/2	ENST00000599180.3	NP_001357016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
FFAR2	ENST00000599180.3 linkuse as main transcript	c.632T>A	p.Leu211His	missense_variant	2/2	1	NM_001370087.1	ENSP00000473159	P1
FFAR2	ENST00000246549.2 linkuse as main transcript	c.632T>A	p.Leu211His	missense_variant	1/1			ENSP00000246549	P1
FFAR2	ENST00000601590.1 linkuse as main transcript	n.17-807T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0547

AC:

8316

AN:

152118

Hom.:

296

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0288

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0302

Gnomad ASJ

AF:

0.0821

Gnomad EAS

AF:

0.000771

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.0662

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0727

Gnomad OTH

AF:

0.0560

GnomAD3 exomes

AF:

0.0636

AC:

15982

AN:

251360

Hom.:

715

AF XY:

0.0684

AC XY:

9300

AN XY:

135886

show subpopulations

Gnomad AFR exome

AF:

0.0278

Gnomad AMR exome

AF:

0.0231

Gnomad ASJ exome

AF:

0.0805

Gnomad EAS exome

AF:

0.000326

Gnomad SAS exome

AF:

0.122

Gnomad FIN exome

AF:

0.0670

Gnomad NFE exome

AF:

0.0735

Gnomad OTH exome

AF:

0.0600

GnomAD4 exome

AF:

0.0735

AC:

107450

AN:

1461880

Hom.:

4485

Cov.:

AF XY:

0.0752

AC XY:

54673

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.0283

Gnomad4 AMR exome

AF:

0.0239

Gnomad4 ASJ exome

AF:

0.0823

Gnomad4 EAS exome

AF:

0.000831

Gnomad4 SAS exome

AF:

0.119

Gnomad4 FIN exome

AF:

0.0723

Gnomad4 NFE exome

AF:

0.0761

Gnomad4 OTH exome

AF:

0.0671

GnomAD4 genome

AF:

0.0546

AC:

8316

AN:

152236

Hom.:

296

Cov.:

AF XY:

0.0544

AC XY:

4052

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.0288

Gnomad4 AMR

AF:

0.0302

Gnomad4 ASJ

AF:

0.0821

Gnomad4 EAS

AF:

0.000773

Gnomad4 SAS

AF:

0.118

Gnomad4 FIN

AF:

0.0662

Gnomad4 NFE

AF:

0.0727

Gnomad4 OTH

AF:

0.0555

Alfa

AF:

0.0692

Hom.:

276

Bravo

AF:

0.0495

TwinsUK

AF:

0.0747

AC:

277

ALSPAC

AF:

0.0833

AC:

321

ESP6500AA

AF:

0.0322

AC:

142

ESP6500EA

AF:

0.0724

AC:

623

ExAC

AF:

0.0656

AC:

7969

Asia WGS

AF:

0.0540

AC:

188

AN:

3478

EpiCase

AF:

0.0713

EpiControl

AF:

0.0708

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.073

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.21

DEOGEN2

Benign

0.015

T;T

Eigen

Benign

-0.77

Eigen_PC

Benign

-0.49

FATHMM_MKL

Benign

0.15

LIST_S2

Benign

0.089

.;T

MetaRNN

Benign

0.0013

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-2.2

N;N

MutationTaster

Benign

1.0

PrimateAI

Benign

0.45

PROVEAN

Benign

4.9

.;N

REVEL

Benign

0.12

Sift

Benign

1.0

.;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.044

MPC

0.24

ClinPred

0.0048

GERP RS

5.5

Varity_R

0.096

gMVP

0.54

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over