chr19-35350955-G-A

Variant names:

• chr19-35350955-G-A
• rs1978014
• NM_005303.3:c.-348+117G>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.-348+117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 151,978 control chromosomes in the GnomAD database, including 35,521 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 0.67 (35521 hom., cov: 31)
• Consequence: FFAR1 NM_005303.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FFAR1	NM_005303.3	c.-348+117G>A		intron_variant	Intron 1 of 1	ENST00000246553.4	NP_005294.1
FFAR1	XM_047438698.1	c.-111+117G>A		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+117G>A		intron_variant	Intron 1 of 1	6	NM_005303.3	ENSP00000246553.2
ENSG00000288731	ENST00000716259.1	n.771-3333C>T		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786314.1	n.648-3333C>T		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786315.1	n.160-3333C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102191 AN: 151858 Hom.: 35467 Cov.: 31

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.673 AC: 102306 AN: 151978 Hom.: 35521 Cov.: 31 AF XY: 0.672 AC XY: 49906 AN XY: 74292

African (AFR) AF: 0.837 AC: 34687 AN: 41456

American (AMR) AF: 0.674 AC: 10298 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2431 AN: 3466

East Asian (EAS) AF: 0.646 AC: 3321 AN: 5144

South Asian (SAS) AF: 0.770 AC: 3701 AN: 4806

European-Finnish (FIN) AF: 0.566 AC: 5982 AN: 10570

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39533 AN: 67930

Other (OTH) AF: 0.689 AC: 1454 AN: 2110

Alfa AF: 0.639 Hom.: 3731

Bravo AF: 0.688

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.60
DANN	Benign	0.26
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1978014; hg19: chr19-35841858;