rs1573611

chr19-35352805-C-T

Variant summary

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

The NM_005303.3(FFAR1):c.*351C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 344,706 control chromosomes in the GnomAD database, including 13,749 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 0.27 (5653 hom., cov: 31)
  • Exomes 𝑓: 0.27 (8096 hom.)
• Consequence: FFAR1 NM_005303.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

Genes affected

FFAR1 (HGNC:4498): (free fatty acid receptor 1) This gene encodes a member of the GP40 family of G protein-coupled receptors that are clustered together on chromosome 19. The encoded protein is a receptor for medium and long chain free fatty acids and may be involved in the metabolic regulation of insulin secretion. Polymorphisms in this gene may be associated with type 2 diabetes. [provided by RefSeq, Apr 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FFAR1	NM_005303.3	c.*351C>T		3_prime_UTR_variant	2/2	ENST00000246553.4
FFAR1	XM_047438698.1	c.*351C>T		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FFAR1	ENST00000246553.4	c.*351C>T		3_prime_UTR_variant	2/2		NM_005303.3	P1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40340 AN: 151896 Hom.: 5649 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.279

GnomAD4 exome AF: 0.271 AC: 52172 AN: 192692 Hom.: 8096 Cov.: 0 AF XY: 0.275 AC XY: 27565 AN XY: 100186

Gnomad4 AFR exome AF: 0.219

Gnomad4 AMR exome AF: 0.342

Gnomad4 ASJ exome AF: 0.266

Gnomad4 EAS exome AF: 0.537

Gnomad4 SAS exome AF: 0.326

Gnomad4 FIN exome AF: 0.283

Gnomad4 NFE exome AF: 0.231

Gnomad4 OTH exome AF: 0.268

GnomAD4 genome AF: 0.266 AC: 40365 AN: 152014 Hom.: 5653 Cov.: 31 AF XY: 0.272 AC XY: 20206 AN XY: 74288

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.284

Alfa AF: 0.253 Hom.: 6459

Bravo AF: 0.266

Asia WGS AF: 0.421 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	3.4
Dann	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1573611; hg19: chr19-35843708;