Variant 10-93601831-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000604414.1(FFAR4):c.697-2243C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 571,988 control chromosomes in the GnomAD database, including 8,772 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 0.14 ( 1680 hom., cov: 33)

Exomes 𝑓: 0.17 ( 7092 hom. )

Consequence

FFAR4
ENST00000604414.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.146

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.24).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FFAR4	ENST00000604414.1 linkuse as main transcript	c.697-2243C>T		intron_variant		3		ENSP00000474477

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20767

AN:

152062

Hom.:

1681

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0683

Gnomad AMI

AF:

0.0614

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.233

Gnomad EAS

AF:

0.0908

Gnomad SAS

AF:

0.328

Gnomad FIN

AF:

0.0957

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.177

GnomAD4 exome

AF:

0.170

AC:

71326

AN:

419808

Hom.:

7092

AF XY:

0.179

AC XY:

40803

AN XY:

227394

show subpopulations

Gnomad4 AFR exome

AF:

0.0717

Gnomad4 AMR exome

AF:

0.126

Gnomad4 ASJ exome

AF:

0.235

Gnomad4 EAS exome

AF:

0.0844

Gnomad4 SAS exome

AF:

0.308

Gnomad4 FIN exome

AF:

0.103

Gnomad4 NFE exome

AF:

0.165

Gnomad4 OTH exome

AF:

0.169

GnomAD4 genome

AF:

0.137

AC:

20793

AN:

152180

Hom.:

1680

Cov.:

AF XY:

0.139

AC XY:

10318

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0684

Gnomad4 AMR

AF:

0.151

Gnomad4 ASJ

AF:

0.233

Gnomad4 EAS

AF:

0.0914

Gnomad4 SAS

AF:

0.329

Gnomad4 FIN

AF:

0.0957

Gnomad4 NFE

AF:

0.166

Gnomad4 OTH

AF:

0.176

Alfa

AF:

0.138

Hom.:

240

Bravo

AF:

0.134

Asia WGS

AF:

0.173

AC:

602

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.24

CADD

Benign

DANN

Benign

0.90

Splicing

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