dbSNP rs77878271: ENSG00000253374:n.299-14617A>G (chr8-81483300-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2

The ENST00000524085.2(ENSG00000253374):n.299-14617A>G variant causes a intron change. The variant allele was found at a frequency of 0.0191 in 474,530 control chromosomes in the GnomAD database, including 133 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 0.016 ( 35 hom., cov: 32)

Exomes 𝑓: 0.020 ( 98 hom. )

Consequence

ENSG00000253374
ENST00000524085.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.39

Publications

11 publications found

Variant links:

Genes affected

ENSG00000253374 (HGNC:):

ENSG00000253374 links:

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0163 (2488/152258) while in subpopulation NFE AF = 0.0224 (1523/68004). AF 95% confidence interval is 0.0215. There are 35 homozygotes in GnomAd4. There are 1291 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 35 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524085.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP4	NM_001442.3	MANE Select	c.-133T>C		upstream_gene	N/A	NP_001433.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000253374	ENST00000524085.2	TSL:5	n.299-14617A>G	intron	N/A
ENSG00000253374	ENST00000832857.1		n.327-38407A>G	intron	N/A
ENSG00000253374	ENST00000832858.1		n.309-38407A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0163

AC:

2485

AN:

152140

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00372

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00943

Gnomad ASJ

AF:

0.0176

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.0532

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0224

Gnomad OTH

AF:

0.0139

GnomAD4 exome

AF:

0.0204

AC:

6582

AN:

322272

Hom.:

Cov.:

AF XY:

0.0200

AC XY:

3331

AN XY:

166470

show subpopulations

African (AFR)

AF:

0.00307

AC:

AN:

8470

American (AMR)

AF:

0.00751

AC:

AN:

9058

Ashkenazi Jewish (ASJ)

AF:

0.0187

AC:

199

AN:

10654

East Asian (EAS)

AF:

0.00

AC:

AN:

24108

South Asian (SAS)

AF:

0.00357

AC:

AN:

13174

European-Finnish (FIN)

AF:

0.0604

AC:

1515

AN:

25092

Middle Eastern (MID)

AF:

0.0101

AC:

AN:

1790

European-Non Finnish (NFE)

AF:

0.0206

AC:

4339

AN:

210502

Other (OTH)

AF:

0.0190

AC:

370

AN:

19424

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

299

598

896

1195

1494

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

144

192

240

<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:

0.0163

AC:

2488

AN:

152258

Hom.:

Cov.:

AF XY:

0.0173

AC XY:

1291

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.00370

AC:

154

AN:

41574

American (AMR)

AF:

0.00955

AC:

146

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0176

AC:

AN:

3464

East Asian (EAS)

AF:

0.00

AC:

AN:

5184

South Asian (SAS)

AF:

0.00187

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0532

AC:

564

AN:

10600

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0224

AC:

1523

AN:

68004

Other (OTH)

AF:

0.0137

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

122

245

367

490

612

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<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:

0.0156

Hom.:

Bravo

AF:

0.0130

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

4.4

PromoterAI

-0.36

Neutral

(source)

Splicing

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