rs10882273

Positions:

• chr10-93589148-T-C

Variant summary

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

The NM_001195755.2(FFAR4):​c.*1539T>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 0.431 in 152,228 control chromosomes in the GnomAD database, including 15,268 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 (15259 hom., cov: 32)
  • Exomes 𝑓: 0.34 (9 hom.)
• Consequence: FFAR4 NM_001195755.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FFAR4	NM_001195755.2	c.*1539T>C		3_prime_UTR_variant	3/3	ENST00000371481.9
FFAR4	NM_181745.4	c.*1539T>C		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FFAR4	ENST00000371481.9	c.*1539T>C		3_prime_UTR_variant	3/3	1	NM_001195755.2	P1
FFAR4	ENST00000371483.8	c.*1539T>C		3_prime_UTR_variant	4/4	1
FFAR4	ENST00000604414.1	c.696+12929T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65453 AN: 152000 Hom.: 15221 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.430

GnomAD4 exome AF: 0.336 AC: 37 AN: 110 Hom.: 9 Cov.: 0 AF XY: 0.330 AC XY: 29 AN XY: 88

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.330

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.431 AC: 65556 AN: 152118 Hom.: 15259 Cov.: 32 AF XY: 0.430 AC XY: 31950 AN XY: 74358

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.425

Alfa AF: 0.390 Hom.: 19517

Bravo AF: 0.432

Asia WGS AF: 0.282 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.37

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

Publications

LitVar

Other links and lift over

dbSNP: rs10882273; hg19: chr10-95348905;