rs10882272

Variant names:

• chr10-93588425-T-C
• rs10882272
• NM_001195755.2:c.*816T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001195755.2(FFAR4):​c.*816T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,152 control chromosomes in the GnomAD database, including 15,513 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 0.43 (15513 hom., cov: 29)
  • Failed GnomAD Quality Control
• Consequence: FFAR4 NM_001195755.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 37 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FFAR4	NM_001195755.2	c.*816T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000371481.9	NP_001182684.1
FFAR4	NM_181745.4	c.*816T>C		3_prime_UTR_variant	Exon 4 of 4		NP_859529.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FFAR4	ENST00000371481.9	c.*816T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_001195755.2	ENSP00000360536.5
FFAR4	ENST00000371483.8	c.*816T>C		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000360538.4
FFAR4	ENST00000604414.1	c.696+12206T>C		intron_variant	Intron 2 of 2	3		ENSP00000474477.1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65492 AN: 151034 Hom.: 15475 Cov.: 29

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.436

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.434 AC: 65595 AN: 151152 Hom.: 15513 Cov.: 29 AF XY: 0.433 AC XY: 31948 AN XY: 73802

African (AFR) AF: 0.621 AC: 25504 AN: 41088

American (AMR) AF: 0.331 AC: 5038 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1513 AN: 3464

East Asian (EAS) AF: 0.114 AC: 584 AN: 5134

South Asian (SAS) AF: 0.420 AC: 2006 AN: 4780

European-Finnish (FIN) AF: 0.385 AC: 3987 AN: 10366

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.378 AC: 25660 AN: 67826

Other (OTH) AF: 0.431 AC: 903 AN: 2096

Alfa AF: 0.392 Hom.: 43026

Bravo AF: 0.436

Asia WGS AF: 0.281 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.79
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10882272; hg19: chr10-95348182;