Variant chr10-93587293-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001195755.2(FFAR4):c.770A>G(p.Gln257Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00289 in 1,614,122 control chromosomes in the GnomAD database, including 109 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0052 ( 20 hom., cov: 31)

Exomes 𝑓: 0.0027 ( 89 hom. )

Consequence

FFAR4
NM_001195755.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.77

Variant links:

Genes affected

FFAR4 (HGNC:19061): (free fatty acid receptor 4) This gene encodes a G protein-coupled receptor (GPR) which belongs to the rhodopsin family of GPRs. The encoded protein functions as a receptor for free fatty acids, including omega-3, and participates in suppressing anti-inflammatory responses and insulin sensitizing. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

FFAR4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0024080873).

BP6

Variant 10-93587293-A-G is Benign according to our data. Variant chr10-93587293-A-G is described in ClinVar as [Benign]. Clinvar id is 708083.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00521 (793/152268) while in subpopulation EAS AF= 0.0219 (113/5166). AF 95% confidence interval is 0.0186. There are 20 homozygotes in gnomad4. There are 567 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 20 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FFAR4	NM_001195755.2 linkuse as main transcript	c.770A>G	p.Gln257Arg	missense_variant	3/3	ENST00000371481.9
FFAR4	NM_181745.4 linkuse as main transcript	c.818A>G	p.Gln273Arg	missense_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FFAR4	ENST00000371481.9 linkuse as main transcript	c.770A>G	p.Gln257Arg	missense_variant	3/3	1	NM_001195755.2	P1	Q5NUL3-2
FFAR4	ENST00000371483.8 linkuse as main transcript	c.818A>G	p.Gln273Arg	missense_variant	4/4	1			Q5NUL3-1
FFAR4	ENST00000604414.1 linkuse as main transcript	c.696+11074A>G		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00521

AC:

792

AN:

152150

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000314

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00105

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0218

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0546

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000867

Gnomad OTH

AF:

0.00479

GnomAD3 exomes

AF:

0.00614

AC:

1545

AN:

251430

Hom.:

AF XY:

0.00601

AC XY:

817

AN XY:

135884

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.000116

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0228

Gnomad SAS exome

AF:

0.000457

Gnomad FIN exome

AF:

0.0445

Gnomad NFE exome

AF:

0.000994

Gnomad OTH exome

AF:

0.00440

GnomAD4 exome

AF:

0.00265

AC:

3879

AN:

1461854

Hom.:

Cov.:

AF XY:

0.00259

AC XY:

1884

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.000112

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0277

Gnomad4 SAS exome

AF:

0.000359

Gnomad4 FIN exome

AF:

0.0410

Gnomad4 NFE exome

AF:

0.000266

Gnomad4 OTH exome

AF:

0.00399

GnomAD4 genome

AF:

0.00521

AC:

793

AN:

152268

Hom.:

Cov.:

AF XY:

0.00761

AC XY:

567

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.000313

Gnomad4 AMR

AF:

0.00105

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0219

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0546

Gnomad4 NFE

AF:

0.000867

Gnomad4 OTH

AF:

0.00522

Alfa

AF:

0.00132

Hom.:

Bravo

AF:

0.00159

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.000349

AC:

ExAC

AF:

0.00553

AC:

672

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.000327

EpiControl

AF:

0.000237

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 submitter

clinical testing

Invitae

Dec 01, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.080

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.73

CADD

Benign

DANN

Benign

0.71

Eigen

Benign

-0.61

Eigen_PC

Benign

-0.37

FATHMM_MKL

Benign

0.68

LIST_S2

Benign

0.61

T;T

MetaRNN

Benign

0.0024

T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

0.60

N;N

PrimateAI

Benign

0.41

PROVEAN

Benign

0.030

N;N

REVEL

Benign

0.069

Sift

Benign

1.0

T;T

Sift4G

Benign

0.84

T;T

Polyphen

0.0

B;B

Vest4

0.045

MVP

0.32

MPC

0.57

ClinPred

0.013

GERP RS

3.9

Varity_R

0.12

gMVP

0.49

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