NM_001442.3:c.73+628C>T

Variant names:

• chr8-81482467-G-A
• rs2290201
• NM_001442.3:c.73+628C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000253374 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FABP4	NM_001442.3	c.73+628C>T		intron_variant	Intron 1 of 3	ENST00000256104.5	NP_001433.1
LOC101927118	XR_001745980.2	n.517+20493G>A		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP4	ENST00000256104.5	c.73+628C>T		intron_variant	Intron 1 of 3	1	NM_001442.3	ENSP00000256104.4

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

African (AFR) AF: 0.684 AC: 28360 AN: 41462

American (AMR) AF: 0.359 AC: 5477 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 931 AN: 3464

East Asian (EAS) AF: 0.743 AC: 3845 AN: 5174

South Asian (SAS) AF: 0.299 AC: 1444 AN: 4822

European-Finnish (FIN) AF: 0.200 AC: 2115 AN: 10580

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18299 AN: 67940

Other (OTH) AF: 0.377 AC: 795 AN: 2108

Alfa AF: 0.362 Hom.: 1574

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
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2290201; hg19: chr8-82394702;