rs10418569

chr19-35351338-T-C

Variant summary

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

The NM_005303.3(FFAR1):c.-214T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,166 control chromosomes in the GnomAD database, including 1,470 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 0.13 (1470 hom., cov: 33)
• Consequence: FFAR1 NM_005303.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FFAR1	NM_005303.3	c.-214T>C		5_prime_UTR_variant	2/2	ENST00000246553.4
FFAR1	XM_047438698.1	c.-110-104T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FFAR1	ENST00000246553.4	c.-214T>C		5_prime_UTR_variant	2/2		NM_005303.3	P1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19117 AN: 152048 Hom.: 1470 Cov.: 33

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.0625

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.141

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.126 AC: 19106 AN: 152166 Hom.: 1470 Cov.: 33 AF XY: 0.123 AC XY: 9177 AN XY: 74378

Gnomad4 AFR AF: 0.0560

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.0626

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.139

Alfa AF: 0.169 Hom.: 1924

Bravo AF: 0.122

Asia WGS AF: 0.0400 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.4
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10418569; hg19: chr19-35842241;