dbSNP rs2305319: FABP4:c.247-124A>G (chr8-81479639-T-C) – 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.247-124A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 607,306 control chromosomes in the GnomAD database, including 7,964 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 0.15 ( 1874 hom., cov: 32)

Exomes 𝑓: 0.16 ( 6090 hom. )

Consequence

FABP4
NM_001442.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.672

Publications

2 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=-0.79).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP4	NM_001442.3 link	c.247-124A>G		intron_variant	Intron 2 of 3	ENST00000256104.5	NP_001433.1	P15090E7DVW4
LOC101927118	XR_001745980.2 link	n.517+17665T>C		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP4	ENST00000256104.5 link	c.247-124A>G		intron_variant	Intron 2 of 3	1	NM_001442.3	ENSP00000256104.4		P15090

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23451

AN:

151970

Hom.:

1867

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.0855

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.170

Gnomad EAS

AF:

0.0677

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.167

Gnomad OTH

AF:

0.148

GnomAD4 exome

AF:

0.156

AC:

70901

AN:

455218

Hom.:

6090

Cov.:

AF XY:

0.159

AC XY:

38126

AN XY:

240198

show subpopulations

African (AFR)

AF:

0.158

AC:

1939

AN:

12284

American (AMR)

AF:

0.144

AC:

2465

AN:

17106

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

2168

AN:

13286

East Asian (EAS)

AF:

0.0618

AC:

1896

AN:

30664

South Asian (SAS)

AF:

0.191

AC:

6988

AN:

36492

European-Finnish (FIN)

AF:

0.133

AC:

4794

AN:

36030

Middle Eastern (MID)

AF:

0.206

AC:

666

AN:

3238

European-Non Finnish (NFE)

AF:

0.163

AC:

45842

AN:

280680

Other (OTH)

AF:

0.163

AC:

4143

AN:

25438

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

2795

5590

8385

11180

13975

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

422

844

1266

1688

2110

<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:

0.154

AC:

23491

AN:

152088

Hom.:

1874

Cov.:

AF XY:

0.152

AC XY:

11286

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.157

AC:

6504

AN:

41468

American (AMR)

AF:

0.142

AC:

2173

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.170

AC:

591

AN:

3468

East Asian (EAS)

AF:

0.0678

AC:

352

AN:

5190

South Asian (SAS)

AF:

0.173

AC:

831

AN:

4816

European-Finnish (FIN)

AF:

0.116

AC:

1228

AN:

10582

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.167

AC:

11365

AN:

67986

Other (OTH)

AF:

0.150

AC:

317

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1016

2033

3049

4066

5082

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.167

Hom.:

260

Bravo

AF:

0.154

Asia WGS

AF:

0.124

AC:

429

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.7

(source)

DANN

Benign

0.72

PhyloP100

0.67

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