Genetic Variant FABP2:c.*318C>T (chr4-119318723-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_000134.4(FABP2):c.*318C>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 0.446 in 241,526 control chromosomes in the GnomAD database, including 24,797 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 0.47 ( 16988 hom., cov: 32)

Exomes 𝑓: 0.41 ( 7809 hom. )

Consequence

FABP2
NM_000134.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0460

Publications

31 publications found

Variant links:

Genes affected

FABP2 (HGNC:3556): (fatty acid binding protein 2) The protein encoded by this gene is an intracellular fatty acid-binding protein that participates in the uptake, intracellular metabolism, and transport of long-chain fatty acids. The encoded protein is also involved in the modulation of cell growth and proliferation. This protein binds saturated long-chain fatty acids with high affinity, and may act as a lipid sensor to maintain energy homeostasis. [provided by RefSeq, Aug 2017]

FABP2 links:

ENSG00000294020 (HGNC:):

ENSG00000294020 links:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000134.4. 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
	FABP2	NM_000134.4	MANE Select	c.*318C>T		3_prime_UTR	Exon 4 of 4	NP_000125.2	P12104

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FABP2	ENST00000274024.4	TSL:1 MANE Select	c.*318C>T	3_prime_UTR	Exon 4 of 4	ENSP00000274024.3	P12104
ENSG00000294020	ENST00000720595.1		n.176-15605G>A	intron	N/A
ENSG00000294020	ENST00000720596.1		n.224-15605G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.468

AC:

70959

AN:

151618

Hom.:

16965

Cov.:

show subpopulations

Gnomad AFR

AF:

0.542

Gnomad AMI

AF:

0.437

Gnomad AMR

AF:

0.394

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.426

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.454

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.458

GnomAD4 exome

AF:

0.409

AC:

36681

AN:

89790

Hom.:

7809

Cov.:

AF XY:

0.398

AC XY:

19466

AN XY:

48924

show subpopulations

African (AFR)

AF:

0.516

AC:

751

AN:

1456

American (AMR)

AF:

0.343

AC:

534

AN:

1556

Ashkenazi Jewish (ASJ)

AF:

0.279

AC:

780

AN:

2792

East Asian (EAS)

AF:

0.369

AC:

1160

AN:

3142

South Asian (SAS)

AF:

0.282

AC:

3505

AN:

12428

European-Finnish (FIN)

AF:

0.443

AC:

2113

AN:

4774

Middle Eastern (MID)

AF:

0.382

AC:

166

AN:

434

European-Non Finnish (NFE)

AF:

0.440

AC:

25438

AN:

57800

Other (OTH)

AF:

0.413

AC:

2234

AN:

5408

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1027

2054

3080

4107

5134

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

180

240

300

<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:

0.468

AC:

71032

AN:

151736

Hom.:

16988

Cov.:

AF XY:

0.463

AC XY:

34342

AN XY:

74142

show subpopulations

African (AFR)

AF:

0.542

AC:

22428

AN:

41360

American (AMR)

AF:

0.394

AC:

6002

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

997

AN:

3468

East Asian (EAS)

AF:

0.426

AC:

2202

AN:

5170

South Asian (SAS)

AF:

0.290

AC:

1396

AN:

4818

European-Finnish (FIN)

AF:

0.454

AC:

4777

AN:

10532

Middle Eastern (MID)

AF:

0.421

AC:

123

AN:

292

European-Non Finnish (NFE)

AF:

0.468

AC:

31745

AN:

67858

Other (OTH)

AF:

0.458

AC:

966

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1917

3833

5750

7666

9583

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

652

1304

1956

2608

3260

<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:

0.460

Hom.:

51645

Bravo

AF:

0.474

Asia WGS

AF:

0.356

AC:

1238

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.3

(source)

DANN

Benign

0.68

PhyloP100

-0.046

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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