rs1978013

Variant names:

• chr19-35350954-T-C
• rs1978013
• NM_005303.3:c.-348+116T>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.-348+116T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,974 control chromosomes in the GnomAD database, including 13,208 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 0.42 (13208 hom., cov: 32)
• Consequence: FFAR1 NM_005303.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FFAR1	NM_005303.3	c.-348+116T>C		intron_variant	Intron 1 of 1	ENST00000246553.4	NP_005294.1
FFAR1	XM_047438698.1	c.-111+116T>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.-348+116T>C		intron_variant	Intron 1 of 1	6	NM_005303.3	ENSP00000246553.2
ENSG00000288731	ENST00000716259.1	n.771-3332A>G		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786314.1	n.648-3332A>G		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786315.1	n.160-3332A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63229 AN: 151856 Hom.: 13206 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.416 AC: 63254 AN: 151974 Hom.: 13208 Cov.: 32 AF XY: 0.419 AC XY: 31116 AN XY: 74274

African (AFR) AF: 0.395 AC: 16353 AN: 41436

American (AMR) AF: 0.474 AC: 7242 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1516 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2278 AN: 5150

South Asian (SAS) AF: 0.405 AC: 1951 AN: 4814

European-Finnish (FIN) AF: 0.440 AC: 4655 AN: 10570

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27779 AN: 67940

Other (OTH) AF: 0.447 AC: 941 AN: 2106

Alfa AF: 0.413 Hom.: 1569

Bravo AF: 0.418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.34
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1978013; hg19: chr19-35841857;