10-93566834-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.444

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]

ACMG classification

Verdict is Benign. Variant got -7 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.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00235 AC: 358 AN: 152222 Hom.: 0 Cov.: 33

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.: 0 AF XY: 0.00226 AC XY: 273 AN XY: 120984

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.: 12 Cov.: 32 AF XY: 0.00288 AC XY: 2077 AN XY: 720364

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.: 0 Cov.: 33 AF XY: 0.00208 AC XY: 155 AN XY: 74482

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.: 0

Bravo AF: 0.00207

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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

Other links and lift over

dbSNP: rs139357642; hg19: chr10-95326591;