chr8-81478525-C-T

Position:

• chr8-81478525-C-T

Variant summary

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

The ENST00000256104.5(FABP4):​c.*340G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 189,768 control chromosomes in the GnomAD database, including 4,074 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 0.17 (3228 hom., cov: 32)
  • Exomes 𝑓: 0.15 (846 hom.)
• Consequence: FABP4 ENST00000256104.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP4	NM_001442.3	c.*340G>A		3_prime_UTR_variant	4/4	ENST00000256104.5	NP_001433.1
LOC101927118	XR_001745980.2	n.517+16551C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FABP4	ENST00000256104.5	c.*340G>A		3_prime_UTR_variant	4/4	1	NM_001442.3	ENSP00000256104	P1
	ENST00000524085.2	n.299-19392C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25946 AN: 151978 Hom.: 3232 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0840

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.165

GnomAD4 exome AF: 0.146 AC: 5486 AN: 37672 Hom.: 846 Cov.: 0 AF XY: 0.146 AC XY: 2861 AN XY: 19568

Gnomad4 AFR exome AF: 0.275

Gnomad4 AMR exome AF: 0.197

Gnomad4 ASJ exome AF: 0.101

Gnomad4 EAS exome AF: 0.670

Gnomad4 SAS exome AF: 0.106

Gnomad4 FIN exome AF: 0.0757

Gnomad4 NFE exome AF: 0.0916

Gnomad4 OTH exome AF: 0.150

GnomAD4 genome AF: 0.171 AC: 25958 AN: 152096 Hom.: 3228 Cov.: 32 AF XY: 0.171 AC XY: 12727 AN XY: 74376

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0988

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0840

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.165

Alfa AF: 0.108 Hom.: 1564

Bravo AF: 0.188

Asia WGS AF: 0.358 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.59

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: rs1054135; hg19: chr8-82390760;