rs16909187

chr8-81478482-G-Achr8-81478482-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FABP4	NM_001442.3	c.*383C>T		3_prime_UTR_variant	4/4	ENST00000256104.5
LOC101927118	XR_001745980.2	n.517+16508G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP4	ENST00000256104.5	c.*383C>T		3_prime_UTR_variant	4/4	1	NM_001442.3	P1
	ENST00000524085.2	n.299-19435G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24173 AN: 151946 Hom.: 1994 Cov.: 32

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.: 0 AF XY: 0.151 AC XY: 792 AN XY: 5246

Gnomad4 AFR exome AF: 0.121

Gnomad4 AMR exome AF: 0.114

Gnomad4 ASJ exome AF: 0.134

Gnomad4 EAS exome AF: 0.0717

Gnomad4 SAS exome AF: 0.205

Gnomad4 FIN exome AF: 0.133

Gnomad4 NFE exome AF: 0.156

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.159 AC: 24226 AN: 152064 Hom.: 2007 Cov.: 32 AF XY: 0.156 AC XY: 11617 AN XY: 74314

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0671

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.161

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
Dann	Benign	0.64

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: rs16909187; hg19: chr8-82390717;