8-81482186-C-T

Variant names:

• chr8-81482186-C-T
• rs7018409
• NM_001442.3:c.73+909G>A

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+909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 151,918 control chromosomes in the GnomAD database, including 1,873 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 (1873 hom., cov: 32)
• Consequence: FABP4 NM_001442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001442.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP4	NM_001442.3	MANE Select	c.73+909G>A		intron	N/A	NP_001433.1	P15090

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP4	ENST00000256104.5	TSL:1 MANE Select	c.73+909G>A		intron	N/A	ENSP00000256104.4	P15090
	FABP4	ENST00000956908.1		c.73+909G>A		intron	N/A	ENSP00000626967.1
	FABP4	ENST00000956910.1		c.73+909G>A		intron	N/A	ENSP00000626969.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23423 AN: 151800 Hom.: 1866 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0672

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.154 AC: 23463 AN: 151918 Hom.: 1873 Cov.: 32 AF XY: 0.152 AC XY: 11265 AN XY: 74248

African (AFR) AF: 0.157 AC: 6498 AN: 41446

American (AMR) AF: 0.142 AC: 2171 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3470

East Asian (EAS) AF: 0.0673 AC: 348 AN: 5168

South Asian (SAS) AF: 0.172 AC: 827 AN: 4804

European-Finnish (FIN) AF: 0.116 AC: 1224 AN: 10552

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11357 AN: 67912

Other (OTH) AF: 0.150 AC: 317 AN: 2110

Alfa AF: 0.160 Hom.: 6928

Bravo AF: 0.154

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		0.033
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: rs7018409; hg19: chr8-82394421;