rs10418569

Variant names:

• chr19-35351338-T-C
• rs10418569
• NM_005303.3:c.-214T>C

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.87).
• 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 rank	MANE	Protein	UniProt
FFAR1	NM_005303.3	c.-214T>C		5_prime_UTR_variant	Exon 2 of 2	ENST00000246553.4	NP_005294.1
FFAR1	XM_047438698.1	c.-110-104T>C		intron_variant	Intron 1 of 1		XP_047294654.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FFAR1	ENST00000246553.4	c.-214T>C		5_prime_UTR_variant	Exon 2 of 2	6	NM_005303.3	ENSP00000246553.2
ENSG00000288731	ENST00000716259.1	n.771-3716A>G		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786314.1	n.648-3716A>G		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786315.1	n.160-3716A>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0560 AC: 2327 AN: 41528

American (AMR) AF: 0.136 AC: 2080 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3468

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5174

South Asian (SAS) AF: 0.0626 AC: 301 AN: 4812

European-Finnish (FIN) AF: 0.136 AC: 1445 AN: 10608

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11850 AN: 67974

Other (OTH) AF: 0.139 AC: 293 AN: 2106

Alfa AF: 0.166 Hom.: 2391

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
PhyloP100		0.093
PromoterAI		0.042	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10418569; hg19: chr19-35842241;