dbSNP rs16909187: FABP4:c.*383C>T (chr8-81478482-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.*383C>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 0.159 in 161,970 control chromosomes in the GnomAD database, including 2,131 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 0.16 ( 2007 hom., cov: 32)

Exomes 𝑓: 0.15 ( 124 hom. )

Consequence

FABP4
NM_001442.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.72

Publications

10 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP4	NM_001442.3 link	c.*383C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000256104.5	NP_001433.1	P15090E7DVW4
LOC101927118	XR_001745980.2 link	n.517+16508G>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.*383C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_001442.3	ENSP00000256104.4		P15090

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24173

AN:

151946

Hom.:

1994

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.0855

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.0670

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.172

Gnomad OTH

AF:

0.158

GnomAD4 exome

AF:

0.148

AC:

1470

AN:

9906

Hom.:

124

Cov.:

AF XY:

0.151

AC XY:

792

AN XY:

5246

show subpopulations

African (AFR)

AF:

0.121

AC:

AN:

248

American (AMR)

AF:

0.114

AC:

121

AN:

1066

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

AN:

290

East Asian (EAS)

AF:

0.0717

AC:

AN:

474

South Asian (SAS)

AF:

0.205

AC:

136

AN:

662

European-Finnish (FIN)

AF:

0.133

AC:

AN:

376

Middle Eastern (MID)

AF:

0.182

AC:

AN:

European-Non Finnish (NFE)

AF:

0.156

AC:

979

AN:

6268

Other (OTH)

AF:

0.154

AC:

AN:

500

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

123

185

246

308

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.159

AC:

24226

AN:

152064

Hom.:

2007

Cov.:

AF XY:

0.156

AC XY:

11617

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.164

AC:

6820

AN:

41494

American (AMR)

AF:

0.146

AC:

2234

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

627

AN:

3468

East Asian (EAS)

AF:

0.0671

AC:

347

AN:

5170

South Asian (SAS)

AF:

0.177

AC:

853

AN:

4818

European-Finnish (FIN)

AF:

0.113

AC:

1191

AN:

10576

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.172

AC:

11684

AN:

67966

Other (OTH)

AF:

0.161

AC:

340

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1047

2094

3141

4188

5235

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

264

528

792

1056

1320

<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:

0.166

Hom.:

324

Bravo

AF:

0.159

Asia WGS

AF:

0.138

AC:

480

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.37

(source)

DANN

Benign

0.64

PhyloP100

-1.7

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