rs767849907

Variant names:

• chr19-35449761-T-A
• NM_001370087.1:c.47T>A

Your query was ambiguous. Multiple possible variants found:

• chr19-35449761-T-A
• chr19-35449761-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001370087.1(FFAR2):​c.47T>A​(p.Ile16Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000139 in 1,440,938 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I16T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: FFAR2 NM_001370087.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.15

Genes affected

FFAR2 (HGNC:4501): (free fatty acid receptor 2) 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 short chain free fatty acids and may be involved in the inflammatory response and in regulating lipid plasma levels. [provided by RefSeq, Apr 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FFAR2	NM_001370087.1	c.47T>A	p.Ile16Asn	missense_variant	Exon 2 of 2	ENST00000599180.3	NP_001357016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FFAR2	ENST00000599180.3	c.47T>A	p.Ile16Asn	missense_variant	Exon 2 of 2	1	NM_001370087.1	ENSP00000473159.1
FFAR2	ENST00000246549.2	c.47T>A	p.Ile16Asn	missense_variant	Exon 1 of 1	6		ENSP00000246549.2
FFAR2	ENST00000601590.1	n.17-1392T>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000139 AC: 2 AN: 1440938 Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1 AN XY: 715660

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000181

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.58
BayesDel_addAF	Benign	-0.074	T
BayesDel_noAF	Benign	-0.34
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.59	D;D
Eigen	Uncertain	0.19
Eigen_PC	Benign	0.089
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.80	.;T
M_CAP	Benign	0.044	D
MetaRNN	Uncertain	0.51	D;D
MetaSVM	Benign	-0.87	T
MutationAssessor	Uncertain	2.3	M;M
PrimateAI	Benign	0.40	T
PROVEAN	Pathogenic	-4.4	.;D
REVEL	Benign	0.23
Sift	Uncertain	0.0050	.;D
Sift4G	Uncertain	0.0040	D;D
Polyphen		0.92	P;P
Vest4		0.46
MutPred		0.48		Loss of stability (P = 0.0291);Loss of stability (P = 0.0291);
MVP		0.69
MPC		0.88
ClinPred		0.97	D
GERP RS		4.7
Varity_R		0.31
gMVP		0.65

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-35940663;