Genetic Variant FABP4:c.74-16C>T (chr8-81480614-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_001442.3(FABP4):c.74-16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 1,593,162 control chromosomes in the GnomAD database, including 18,761 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 0.12 ( 1336 hom., cov: 32)

Exomes 𝑓: 0.15 ( 17425 hom. )

Consequence

FABP4
NM_001442.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0140

Publications

9 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=-0.72).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP4	NM_001442.3 link	c.74-16C>T		intron_variant	Intron 1 of 3	ENST00000256104.5	NP_001433.1	P15090E7DVW4
LOC101927118	XR_001745980.2 link	n.517+18640G>A		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP4	ENST00000256104.5 link	c.74-16C>T		intron_variant	Intron 1 of 3	1	NM_001442.3	ENSP00000256104.4		P15090

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18828

AN:

152018

Hom.:

1333

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0773

Gnomad AMI

AF:

0.0855

Gnomad AMR

AF:

0.0968

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.143

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.124

GnomAD2 exomes

AF:

0.125

AC:

29465

AN:

236394

AF XY:

0.131

show subpopulations

Gnomad AFR exome

AF:

0.0733

Gnomad AMR exome

AF:

0.0616

Gnomad ASJ exome

AF:

0.152

Gnomad EAS exome

AF:

0.000391

Gnomad FIN exome

AF:

0.125

Gnomad NFE exome

AF:

0.160

Gnomad OTH exome

AF:

0.138

GnomAD4 exome

AF:

0.150

AC:

215504

AN:

1441026

Hom.:

17425

Cov.:

AF XY:

0.151

AC XY:

108257

AN XY:

715420

show subpopulations

African (AFR)

AF:

0.0751

AC:

2448

AN:

32594

American (AMR)

AF:

0.0672

AC:

2815

AN:

41882

Ashkenazi Jewish (ASJ)

AF:

0.158

AC:

3955

AN:

25104

East Asian (EAS)

AF:

0.000482

AC:

AN:

39390

South Asian (SAS)

AF:

0.165

AC:

13706

AN:

83248

European-Finnish (FIN)

AF:

0.133

AC:

7004

AN:

52776

Middle Eastern (MID)

AF:

0.183

AC:

1030

AN:

5622

European-Non Finnish (NFE)

AF:

0.160

AC:

175854

AN:

1100966

Other (OTH)

AF:

0.146

AC:

8673

AN:

59444

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

7862

15724

23586

31448

39310

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6108

12216

18324

24432

30540

<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:

0.124

AC:

18840

AN:

152136

Hom.:

1336

Cov.:

AF XY:

0.121

AC XY:

9012

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.0772

AC:

3205

AN:

41524

American (AMR)

AF:

0.0968

AC:

1480

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

564

AN:

3468

East Asian (EAS)

AF:

0.00174

AC:

AN:

5178

South Asian (SAS)

AF:

0.145

AC:

698

AN:

4822

European-Finnish (FIN)

AF:

0.116

AC:

1223

AN:

10570

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.166

AC:

11283

AN:

67962

Other (OTH)

AF:

0.123

AC:

259

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

795

1590

2385

3180

3975

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<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:

0.152

Hom.:

598

Bravo

AF:

0.117

Asia WGS

AF:

0.0550

AC:

193

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

3.7

(source)

DANN

Benign

0.75

PhyloP100

0.014

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