chr8-81479639-T-C

Position:

• chr8-81479639-T-C

Variant summary

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

The NM_001442.3(FABP4):​c.247-124A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 607,306 control chromosomes in the GnomAD database, including 7,964 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 0.15 (1874 hom., cov: 32)
  • Exomes 𝑓: 0.16 (6090 hom.)
• Consequence: FABP4 NM_001442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.672

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP4	NM_001442.3	c.247-124A>G		intron_variant		ENST00000256104.5	NP_001433.1
LOC101927118	XR_001745980.2	n.517+17665T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FABP4	ENST00000256104.5	c.247-124A>G		intron_variant		1	NM_001442.3	ENSP00000256104.4

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23451 AN: 151970 Hom.: 1867 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0677

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.148

GnomAD4 exome AF: 0.156 AC: 70901 AN: 455218 Hom.: 6090 Cov.: 6 AF XY: 0.159 AC XY: 38126 AN XY: 240198

Gnomad4 AFR exome AF: 0.158

Gnomad4 AMR exome AF: 0.144

Gnomad4 ASJ exome AF: 0.163

Gnomad4 EAS exome AF: 0.0618

Gnomad4 SAS exome AF: 0.191

Gnomad4 FIN exome AF: 0.133

Gnomad4 NFE exome AF: 0.163

Gnomad4 OTH exome AF: 0.163

GnomAD4 genome AF: 0.154 AC: 23491 AN: 152088 Hom.: 1874 Cov.: 32 AF XY: 0.152 AC XY: 11286 AN XY: 74352

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0678

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.150

Alfa AF: 0.167 Hom.: 260

Bravo AF: 0.154

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.7
DANN	Benign	0.72

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: rs2305319; hg19: chr8-82391874;