Variant chr10-93566834-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001195755.2(FFAR4):c.114G>A(p.Val38=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00287 in 1,601,242 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0024 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0029 ( 12 hom. )

Consequence

FFAR4
NM_001195755.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.444

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 10-93566834-G-A is Benign according to our data. Variant chr10-93566834-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2640700.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.444 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
FFAR4	NM_001195755.2 linkuse as main transcript	c.114G>A	p.Val38=	synonymous_variant	1/3	ENST00000371481.9
FFAR4	NM_181745.4 linkuse as main transcript	c.114G>A	p.Val38=	synonymous_variant	1/4
FFAR4	XM_011539746.4 linkuse as main transcript	c.114G>A	p.Val38=	synonymous_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FFAR4	ENST00000371481.9 linkuse as main transcript	c.114G>A	p.Val38=	synonymous_variant	1/3	1	NM_001195755.2	P1	Q5NUL3-2
FFAR4	ENST00000371483.8 linkuse as main transcript	c.114G>A	p.Val38=	synonymous_variant	1/4	1			Q5NUL3-1
FFAR4	ENST00000604414.1 linkuse as main transcript	c.114G>A	p.Val38=	synonymous_variant	1/3	3

Frequencies

GnomAD3 genomes

AF:

0.00235

AC:

358

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000386

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00196

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00198

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00410

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.00237

AC:

525

AN:

221180

Hom.:

AF XY:

0.00226

AC XY:

273

AN XY:

120984

show subpopulations

Gnomad AFR exome

AF:

0.000223

Gnomad AMR exome

AF:

0.000912

Gnomad ASJ exome

AF:

0.00284

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000106

Gnomad FIN exome

AF:

0.00279

Gnomad NFE exome

AF:

0.00407

Gnomad OTH exome

AF:

0.00271

GnomAD4 exome

AF:

0.00293

AC:

4242

AN:

1448902

Hom.:

Cov.:

AF XY:

0.00288

AC XY:

2077

AN XY:

720364

show subpopulations

Gnomad4 AFR exome

AF:

0.000422

Gnomad4 AMR exome

AF:

0.000959

Gnomad4 ASJ exome

AF:

0.00247

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000944

Gnomad4 FIN exome

AF:

0.00332

Gnomad4 NFE exome

AF:

0.00346

Gnomad4 OTH exome

AF:

0.00204

GnomAD4 genome

AF:

0.00235

AC:

358

AN:

152340

Hom.:

Cov.:

AF XY:

0.00208

AC XY:

155

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.000385

Gnomad4 AMR

AF:

0.00196

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00198

Gnomad4 NFE

AF:

0.00410

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.00313

Hom.:

Bravo

AF:

0.00207

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2022

FFAR4: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

5.2

DANN

Benign

0.78

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