10-93604276-C-G

Position:

• chr10-93604276-C-G

Variant summary

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

The ENST00000604414.1(FFAR4):​c.*188C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 392,934 control chromosomes in the GnomAD database, including 946 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 0.074 (668 hom., cov: 33)
  • Exomes 𝑓: 0.040 (278 hom.)
• Consequence: FFAR4 ENST00000604414.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.93604276C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FFAR4	ENST00000604414.1	c.*188C>G		3_prime_UTR_variant	3/3	3		ENSP00000474477.1

Frequencies

GnomAD3 genomes AF: 0.0734 AC: 11158 AN: 152020 Hom.: 661 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.0699

Gnomad SAS AF: 0.0624

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0335

Gnomad OTH AF: 0.0664

GnomAD4 exome AF: 0.0402 AC: 9687 AN: 240796 Hom.: 278 Cov.: 0 AF XY: 0.0396 AC XY: 4835 AN XY: 122040

Gnomad4 AFR exome AF: 0.160

Gnomad4 AMR exome AF: 0.0384

Gnomad4 ASJ exome AF: 0.0534

Gnomad4 EAS exome AF: 0.0553

Gnomad4 SAS exome AF: 0.0619

Gnomad4 FIN exome AF: 0.0130

Gnomad4 NFE exome AF: 0.0330

Gnomad4 OTH exome AF: 0.0585

GnomAD4 genome AF: 0.0736 AC: 11191 AN: 152138 Hom.: 668 Cov.: 33 AF XY: 0.0724 AC XY: 5385 AN XY: 74392

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.0470

Gnomad4 ASJ AF: 0.0623

Gnomad4 EAS AF: 0.0699

Gnomad4 SAS AF: 0.0629

Gnomad4 FIN AF: 0.0129

Gnomad4 NFE AF: 0.0335

Gnomad4 OTH AF: 0.0733

Alfa AF: 0.0113 Hom.: 4

Bravo AF: 0.0790

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17108993; hg19: chr10-95364033;