rs2290201

Positions:

• chr8-81482467-G-A
• chr8-81482467-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.73+628C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,018 control chromosomes in the GnomAD database, including 15,351 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 0.40 (15351 hom., cov: 32)
• Consequence: FABP4 NM_001442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP4	NM_001442.3	c.73+628C>T		intron_variant		ENST00000256104.5	NP_001433.1
LOC101927118	XR_001745980.2	n.517+20493G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FABP4	ENST00000256104.5	c.73+628C>T		intron_variant		1	NM_001442.3	ENSP00000256104	P1
	ENST00000524085.2	n.299-15450G>A		intron_variant, non_coding_transcript_variant		5
FABP4	ENST00000522659.1	c.69+632C>T		intron_variant, NMD_transcript_variant		3		ENSP00000428385
FABP4	ENST00000518669.5	n.142+628C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61334 AN: 151898 Hom.: 15302 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.375

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.404 AC: 61444 AN: 152018 Hom.: 15351 Cov.: 32 AF XY: 0.400 AC XY: 29693 AN XY: 74306

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.377

Alfa AF: 0.350 Hom.: 1403

Bravo AF: 0.433

Asia WGS AF: 0.515 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.053
DANN	Benign	0.51

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: rs2290201; hg19: chr8-82394702;