ENST00000604414.1:c.*188C>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000604414.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FFAR4	ENST00000604414.1	TSL:3	c.*188C>G		3_prime_UTR	Exon 3 of 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

African (AFR) AF: 0.160 AC: 1132 AN: 7080

American (AMR) AF: 0.0384 AC: 280 AN: 7284

Ashkenazi Jewish (ASJ) AF: 0.0534 AC: 486 AN: 9104

East Asian (EAS) AF: 0.0553 AC: 1248 AN: 22574

South Asian (SAS) AF: 0.0619 AC: 133 AN: 2148

European-Finnish (FIN) AF: 0.0130 AC: 262 AN: 20136

Middle Eastern (MID) AF: 0.0722 AC: 91 AN: 1260

European-Non Finnish (NFE) AF: 0.0330 AC: 5116 AN: 155172

Other (OTH) AF: 0.0585 AC: 939 AN: 16038

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

African (AFR) AF: 0.168 AC: 6960 AN: 41494

American (AMR) AF: 0.0470 AC: 718 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0623 AC: 216 AN: 3466

East Asian (EAS) AF: 0.0699 AC: 361 AN: 5168

South Asian (SAS) AF: 0.0629 AC: 302 AN: 4804

European-Finnish (FIN) AF: 0.0129 AC: 137 AN: 10600

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0335 AC: 2279 AN: 68000

Other (OTH) AF: 0.0733 AC: 155 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.26
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17108993; hg19: chr10-95364033;