dbSNP rs1573611: FFAR1:c.*351C>T (chr19-35352805-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005303.3(FFAR1):c.*351C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 344,706 control chromosomes in the GnomAD database, including 13,749 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 0.27 ( 5653 hom., cov: 31)

Exomes 𝑓: 0.27 ( 8096 hom. )

Consequence

FFAR1
NM_005303.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0440

Publications

17 publications found

Variant links:

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]

FFAR1 links:

ENSG00000288731 (HGNC:):

ENSG00000288731 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005303.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FFAR1	NM_005303.3	MANE Select	c.*351C>T		3_prime_UTR	Exon 2 of 2	NP_005294.1	O14842

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FFAR1	ENST00000246553.4	TSL:6 MANE Select	c.*351C>T	3_prime_UTR	Exon 2 of 2	ENSP00000246553.2	O14842
FFAR1	ENST00000950226.1		c.*351C>T	3_prime_UTR	Exon 2 of 2	ENSP00000620285.1
ENSG00000288731	ENST00000716259.1		n.771-5183G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40340

AN:

151896

Hom.:

5649

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.334

Gnomad ASJ

AF:

0.273

Gnomad EAS

AF:

0.526

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.320

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.244

Gnomad OTH

AF:

0.279

GnomAD4 exome

AF:

0.271

AC:

52172

AN:

192692

Hom.:

8096

Cov.:

AF XY:

0.275

AC XY:

27565

AN XY:

100186

show subpopulations

African (AFR)

AF:

0.219

AC:

1528

AN:

6990

American (AMR)

AF:

0.342

AC:

2763

AN:

8090

Ashkenazi Jewish (ASJ)

AF:

0.266

AC:

1648

AN:

6194

East Asian (EAS)

AF:

0.537

AC:

6225

AN:

11590

South Asian (SAS)

AF:

0.326

AC:

6999

AN:

21494

European-Finnish (FIN)

AF:

0.283

AC:

2822

AN:

9988

Middle Eastern (MID)

AF:

0.319

AC:

284

AN:

890

European-Non Finnish (NFE)

AF:

0.231

AC:

26871

AN:

116142

Other (OTH)

AF:

0.268

AC:

3032

AN:

11314

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1728

3456

5183

6911

8639

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

304

608

912

1216

1520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.266

AC:

40365

AN:

152014

Hom.:

5653

Cov.:

AF XY:

0.272

AC XY:

20206

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.214

AC:

8878

AN:

41474

American (AMR)

AF:

0.334

AC:

5102

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.273

AC:

947

AN:

3470

East Asian (EAS)

AF:

0.526

AC:

2714

AN:

5156

South Asian (SAS)

AF:

0.378

AC:

1822

AN:

4814

European-Finnish (FIN)

AF:

0.320

AC:

3375

AN:

10556

Middle Eastern (MID)

AF:

0.323

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.244

AC:

16578

AN:

67952

Other (OTH)

AF:

0.284

AC:

596

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1499

2997

4496

5994

7493

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

414

828

1242

1656

2070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.253

Hom.:

8203

Bravo

AF:

0.266

Asia WGS

AF:

0.421

AC:

1463

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

3.4

(source)

DANN

Benign

0.49

PhyloP100

-0.044

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over