rs16970264

Variant names:

• chr19-35349572-G-A
• rs16970264
• NM_005303.3:c.-1614G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ENSG00000288731 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FFAR1	NM_005303.3	c.-1614G>A		5_prime_UTR_variant	Exon 1 of 2	ENST00000246553.4	NP_005294.1
FFAR1	XM_047438698.1	c.-1377G>A		5_prime_UTR_variant	Exon 1 of 2		XP_047294654.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FFAR1	ENST00000246553.4	c.-1614G>A		5_prime_UTR_variant	Exon 1 of 2	6	NM_005303.3	ENSP00000246553.2
ENSG00000288731	ENST00000716259.1	n.771-1950C>T		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786314.1	n.648-1950C>T		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786315.1	n.160-1950C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.123 AC: 5109 AN: 41560

American (AMR) AF: 0.0570 AC: 872 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3472

East Asian (EAS) AF: 0.110 AC: 571 AN: 5168

South Asian (SAS) AF: 0.225 AC: 1087 AN: 4832

European-Finnish (FIN) AF: 0.0519 AC: 550 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0624 AC: 4244 AN: 68020

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0704 Hom.: 675

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs16970264; hg19: chr19-35840475;