rs17108993

Variant names:

• chr10-93604276-C-G
• rs17108993
• ENST00000604414.1:c.*188C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-93604276-C-G
• chr10-93604276-C-T

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]

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FFAR4	ENST00000604414.1	c.*188C>G		3_prime_UTR_variant	Exon 3 of 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;