rs16909192

Variant names:

• chr8-81478608-A-C
• rs16909192
• NM_001442.3:c.*257T>G

Variant summary

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

The NM_001442.3(FABP4):​c.*257T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 368,384 control chromosomes in the GnomAD database, including 4,193 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 0.13 (1405 hom., cov: 32)
  • Exomes 𝑓: 0.14 (2788 hom.)
• Consequence: FABP4 NM_001442.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.663

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP4	NM_001442.3	c.*257T>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000256104.5	NP_001433.1
LOC101927118	XR_001745980.2	n.517+16634A>C		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP4	ENST00000256104	c.*257T>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_001442.3	ENSP00000256104.4

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19271 AN: 152080 Hom.: 1402 Cov.: 32

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0978

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.144 AC: 31176 AN: 216186 Hom.: 2788 Cov.: 0 AF XY: 0.148 AC XY: 16359 AN XY: 110872

Gnomad4 AFR exome AF: 0.0697

Gnomad4 AMR exome AF: 0.0812

Gnomad4 ASJ exome AF: 0.166

Gnomad4 EAS exome AF: 0.000383

Gnomad4 SAS exome AF: 0.170

Gnomad4 FIN exome AF: 0.135

Gnomad4 NFE exome AF: 0.169

Gnomad4 OTH exome AF: 0.150

GnomAD4 genome AF: 0.127 AC: 19283 AN: 152198 Hom.: 1405 Cov.: 32 AF XY: 0.124 AC XY: 9194 AN XY: 74406

Gnomad4 AFR AF: 0.0786

Gnomad4 AMR AF: 0.0978

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.128

Alfa AF: 0.158 Hom.: 528

Bravo AF: 0.120

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.7
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: rs16909192; hg19: chr8-82390843;