rs12219199

Positions:

• chr10-93572760-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001195755.2(FFAR4):​c.568-3331C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,070 control chromosomes in the GnomAD database, including 1,206 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 0.10 (1206 hom., cov: 32)
• Consequence: FFAR4 NM_001195755.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

FFAR4 (HGNC:19061): (free fatty acid receptor 4) This gene encodes a G protein-coupled receptor (GPR) which belongs to the rhodopsin family of GPRs. The encoded protein functions as a receptor for free fatty acids, including omega-3, and participates in suppressing anti-inflammatory responses and insulin sensitizing. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FFAR4	NM_001195755.2	c.568-3331C>T		intron_variant		ENST00000371481.9	NP_001182684.1
FFAR4	NM_181745.4	c.568-3331C>T		intron_variant			NP_859529.2
FFAR4	XM_011539746.4	c.568-3331C>T		intron_variant			XP_011538048.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FFAR4	ENST00000371481.9	c.568-3331C>T		intron_variant		1	NM_001195755.2	ENSP00000360536.5
FFAR4	ENST00000371483.8	c.568-3331C>T		intron_variant		1		ENSP00000360538.4
FFAR4	ENST00000604414.1	c.568-3331C>T		intron_variant		3		ENSP00000474477.1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15284 AN: 151952 Hom.: 1200 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0819

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

GnomAD4 genome AF: 0.101 AC: 15315 AN: 152070 Hom.: 1206 Cov.: 32 AF XY: 0.102 AC XY: 7564 AN XY: 74342

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.0969

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.0245

Gnomad4 NFE AF: 0.0525

Gnomad4 OTH AF: 0.0810

Alfa AF: 0.0701 Hom.: 922

Bravo AF: 0.109

Asia WGS AF: 0.259 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.075
DANN	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12219199; hg19: chr10-95332517;