rs1978013

chr19-35350954-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.-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

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 (AMR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FFAR1	NM_005303.3	c.-348+116T>C		intron_variant		ENST00000246553.4
FFAR1	XM_047438698.1	c.-111+116T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FFAR1	ENST00000246553.4	c.-348+116T>C		intron_variant			NM_005303.3	P1

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

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.447

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1978013; hg19: chr19-35841857;