Genetic Variant FABP4:c.*340G>A (chr8-81478525-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_001442.3(FABP4):c.*340G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 189,768 control chromosomes in the GnomAD database, including 4,074 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 0.17 ( 3228 hom., cov: 32)

Exomes 𝑓: 0.15 ( 846 hom. )

Consequence

FABP4
NM_001442.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.447

Publications

25 publications found

Variant links:

Genes affected

FABP4 (HGNC:3559): (fatty acid binding protein 4) FABP4 encodes the fatty acid binding protein found in adipocytes. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. [provided by RefSeq, Jul 2008]

FABP4 Gene-Disease associations (from GenCC):

schizophrenia
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

FABP4 links:

ENSG00000253374 (HGNC:):

ENSG00000253374 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP4	NM_001442.3 link	c.*340G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000256104.5	NP_001433.1
LOC101927118	XR_001745980.2 link	n.517+16551C>T		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP4	ENST00000256104.5 link	c.*340G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_001442.3	ENSP00000256104.4

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

25946

AN:

151978

Hom.:

3232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.0988

Gnomad EAS

AF:

0.664

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.0840

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.165

GnomAD4 exome

AF:

0.146

AC:

5486

AN:

37672

Hom.:

846

Cov.:

AF XY:

0.146

AC XY:

2861

AN XY:

19568

show subpopulations

African (AFR)

AF:

0.275

AC:

373

AN:

1356

American (AMR)

AF:

0.197

AC:

425

AN:

2152

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

144

AN:

1426

East Asian (EAS)

AF:

0.670

AC:

1636

AN:

2440

South Asian (SAS)

AF:

0.106

AC:

185

AN:

1750

European-Finnish (FIN)

AF:

0.0757

AC:

134

AN:

1770

Middle Eastern (MID)

AF:

0.0824

AC:

AN:

182

European-Non Finnish (NFE)

AF:

0.0916

AC:

2224

AN:

24268

Other (OTH)

AF:

0.150

AC:

350

AN:

2328

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

195

390

586

781

976

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

160

200

<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:

0.171

AC:

25958

AN:

152096

Hom.:

3228

Cov.:

AF XY:

0.171

AC XY:

12727

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.260

AC:

10787

AN:

41460

American (AMR)

AF:

0.174

AC:

2656

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0988

AC:

343

AN:

3472

East Asian (EAS)

AF:

0.663

AC:

3425

AN:

5168

South Asian (SAS)

AF:

0.125

AC:

602

AN:

4822

European-Finnish (FIN)

AF:

0.0840

AC:

889

AN:

10588

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6862

AN:

67994

Other (OTH)

AF:

0.165

AC:

348

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

994

1989

2983

3978

4972

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<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:

0.110

Hom.:

2191

Bravo

AF:

0.188

Asia WGS

AF:

0.358

AC:

1245

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

(source)

DANN

Benign

0.59

PhyloP100

-0.45

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over