rs8192688

Variant names:

• chr8-81480614-G-A
• rs8192688
• NM_001442.3:c.74-16C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

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]

ENSG00000253859 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	c.74-16C>T		intron_variant	Intron 1 of 3	ENST00000256104.5	NP_001433.1
LOC101927118	XR_001745980.2	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	c.74-16C>T		intron_variant	Intron 1 of 3	1	NM_001442.3	ENSP00000256104.4
FABP4	ENST00000518669.5	n.143-150C>T		intron_variant	Intron 1 of 3	3
FABP4	ENST00000522659.1	n.70-16C>T		intron_variant	Intron 1 of 3	3		ENSP00000428385.1
ENSG00000253859	ENST00000524085.2	n.299-17303G>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18828 AN: 152018 Hom.: 1333 Cov.: 32

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

GnomAD3 exomes AF: 0.125 AC: 29465 AN: 236394 Hom.: 2126 AF XY: 0.131 AC XY: 16754 AN XY: 127732

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 SAS exome AF: 0.154

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.: 31 AF XY: 0.151 AC XY: 108257 AN XY: 715420

Gnomad4 AFR exome AF: 0.0751

Gnomad4 AMR exome AF: 0.0672

Gnomad4 ASJ exome AF: 0.158

Gnomad4 EAS exome AF: 0.000482

Gnomad4 SAS exome AF: 0.165

Gnomad4 FIN exome AF: 0.133

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.146

GnomAD4 genome AF: 0.124 AC: 18840 AN: 152136 Hom.: 1336 Cov.: 32 AF XY: 0.121 AC XY: 9012 AN XY: 74368

Gnomad4 AFR AF: 0.0772

Gnomad4 AMR AF: 0.0968

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.123

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
DANN	Benign	0.75

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

LitVar

Other links and lift over

dbSNP: rs8192688; hg19: chr8-82392849;