rs34571439

Positions:

• chr10-93591553-A-C
• chr10-93591553-A-G

Variant summary

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

The ENST00000604414.1(FFAR4):​c.697-12521A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 157,126 control chromosomes in the GnomAD database, including 4,933 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 0.24 (4848 hom., cov: 32)
  • Exomes 𝑓: 0.15 (85 hom.)
• Consequence: FFAR4 ENST00000604414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.93591553A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FFAR4	ENST00000604414.1	c.697-12521A>C		intron_variant		3		ENSP00000474477.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35859 AN: 151814 Hom.: 4836 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.152 AC: 789 AN: 5194 Hom.: 85 AF XY: 0.146 AC XY: 414 AN XY: 2836

Gnomad4 AFR exome AF: 0.364

Gnomad4 AMR exome AF: 0.164

Gnomad4 ASJ exome AF: 0.400

Gnomad4 EAS exome AF: 0.0833

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.0714

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.184

GnomAD4 genome AF: 0.236 AC: 35922 AN: 151932 Hom.: 4848 Cov.: 32 AF XY: 0.238 AC XY: 17708 AN XY: 74256

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.249

Alfa AF: 0.190 Hom.: 2740

Bravo AF: 0.242

Asia WGS AF: 0.212 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34571439; hg19: chr10-95351310;