rs10423648

Variant names:

• chr19-35347840-A-G
• rs10423648
• ENST00000716259.1:n.771-218T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000716259.1(ENSG00000288731):​n.771-218T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,260 control chromosomes in the GnomAD database, including 1,183 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 0.11 (1183 hom., cov: 32)
• Consequence: ENSG00000288731 ENST00000716259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 9 publications found

Genes affected

ENSG00000288731 (HGNC:):

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

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 = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FFAR1	NM_005303.3	c.-3346A>G		upstream_gene_variant		ENST00000246553.4	NP_005294.1
FFAR1	XM_047438698.1	c.-3109A>G		upstream_gene_variant			XP_047294654.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288731	ENST00000716259.1	n.771-218T>C		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786314.1	n.648-218T>C		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786315.1	n.160-218T>C		intron_variant	Intron 2 of 2
FFAR1	ENST00000246553.4	c.-3346A>G		upstream_gene_variant		6	NM_005303.3	ENSP00000246553.2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16237 AN: 152142 Hom.: 1170 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0621

Gnomad OTH AF: 0.0845

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

GnomAD4 genome AF: 0.107 AC: 16290 AN: 152260 Hom.: 1183 Cov.: 32 AF XY: 0.108 AC XY: 8072 AN XY: 74464

African (AFR) AF: 0.196 AC: 8121 AN: 41510

American (AMR) AF: 0.0674 AC: 1031 AN: 15306

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

East Asian (EAS) AF: 0.119 AC: 616 AN: 5178

South Asian (SAS) AF: 0.226 AC: 1090 AN: 4818

European-Finnish (FIN) AF: 0.0521 AC: 553 AN: 10622

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0621 AC: 4227 AN: 68032

Other (OTH) AF: 0.0922 AC: 195 AN: 2116

Alfa AF: 0.0790 Hom.: 361

Bravo AF: 0.108

Asia WGS AF: 0.216 AC: 750 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	4.0
DANN	Benign	0.44
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10423648; hg19: chr19-35838743;