rs12766992

Variant names:

• chr10-93590359-C-T
• rs12766992
• ENST00000604414.1:c.697-13715C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000604414.1(FFAR4):​c.697-13715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,128 control chromosomes in the GnomAD database, including 2,035 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 0.15 (2035 hom., cov: 32)
• Consequence: FFAR4 ENST00000604414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FFAR4	ENST00000604414.1	c.697-13715C>T		intron_variant	Intron 2 of 2	3		ENSP00000474477.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23302 AN: 152008 Hom.: 2037 Cov.: 32

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.0628

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.191

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.153 AC: 23324 AN: 152128 Hom.: 2035 Cov.: 32 AF XY: 0.157 AC XY: 11685 AN XY: 74356

Gnomad4 AFR AF: 0.0831

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.190

Alfa AF: 0.183 Hom.: 1857

Bravo AF: 0.148

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12766992; hg19: chr10-95350116;