8-81480931-G-T

Variant names:

• chr8-81480931-G-T
• rs10808846
• NM_001442.3:c.74-333C>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.74-333C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,952 control chromosomes in the GnomAD database, including 11,989 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 0.37 (11989 hom., cov: 32)
• Consequence: FABP4 NM_001442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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.74-333C>A		intron	N/A	NP_001433.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP4	ENST00000256104.5	TSL:1 MANE Select	c.74-333C>A		intron	N/A	ENSP00000256104.4
	FABP4	ENST00000956908.1		c.74-333C>A		intron	N/A	ENSP00000626967.1
	FABP4	ENST00000956910.1		c.74-336C>A		intron	N/A	ENSP00000626969.1

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55844 AN: 151836 Hom.: 11957 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.368 AC: 55934 AN: 151952 Hom.: 11989 Cov.: 32 AF XY: 0.365 AC XY: 27112 AN XY: 74286

African (AFR) AF: 0.561 AC: 23243 AN: 41430

American (AMR) AF: 0.339 AC: 5169 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3470

East Asian (EAS) AF: 0.744 AC: 3849 AN: 5176

South Asian (SAS) AF: 0.299 AC: 1436 AN: 4802

European-Finnish (FIN) AF: 0.200 AC: 2110 AN: 10542

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18269 AN: 67954

Other (OTH) AF: 0.351 AC: 741 AN: 2114

Alfa AF: 0.321 Hom.: 16757

Bravo AF: 0.392

Asia WGS AF: 0.507 AC: 1757 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.85
DANN	Benign	0.37
PhyloP100		-1.1
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: rs10808846; hg19: chr8-82393166; COSMIC: COSV56269102; COSMIC: COSV56269102;