rs16970264

chr19-35349572-G-A

Variant summary

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

The NM_005303.3(FFAR1):c.-1614G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0857 in 152,274 control chromosomes in the GnomAD database, including 672 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 0.086 (672 hom., cov: 33)
• Consequence: FFAR1 NM_005303.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FFAR1	NM_005303.3	c.-1614G>A		5_prime_UTR_variant	1/2	ENST00000246553.4
FFAR1	XM_047438698.1	c.-1377G>A		5_prime_UTR_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FFAR1	ENST00000246553.4	c.-1614G>A		5_prime_UTR_variant	1/2		NM_005303.3	P1

Frequencies

GnomAD3 genomes AF: 0.0855 AC: 13015 AN: 152156 Hom.: 661 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.0736

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

GnomAD4 genome AF: 0.0857 AC: 13056 AN: 152274 Hom.: 672 Cov.: 33 AF XY: 0.0879 AC XY: 6542 AN XY: 74454

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0570

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0624

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0684 Hom.: 456

Bravo AF: 0.0842

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.1
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16970264; hg19: chr19-35840475;