rs8192688

Variant names:

• chr8-81480614-G-A
• rs8192688
• NM_001442.3:c.74-16C>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.74-16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 1,593,162 control chromosomes in the GnomAD database, including 18,761 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 0.12 (1336 hom., cov: 32)
  • Exomes 𝑓: 0.15 (17425 hom.)
• Consequence: FABP4 NM_001442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 9 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=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 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.74-16C>T		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.74-16C>T		intron	N/A	ENSP00000256104.4	P15090
	FABP4	ENST00000956908.1		c.74-16C>T		intron	N/A	ENSP00000626967.1
	FABP4	ENST00000956910.1		c.74-19C>T		intron	N/A	ENSP00000626969.1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18828 AN: 152018 Hom.: 1333 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0968

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.124

GnomAD2 exomes AF: 0.125 AC: 29465 AN: 236394 AF XY: 0.131

Gnomad AFR exome AF: 0.0733

Gnomad AMR exome AF: 0.0616

Gnomad ASJ exome AF: 0.152

Gnomad EAS exome AF: 0.000391

Gnomad FIN exome AF: 0.125

Gnomad NFE exome AF: 0.160

Gnomad OTH exome AF: 0.138

GnomAD4 exome AF: 0.150 AC: 215504 AN: 1441026 Hom.: 17425 Cov.: 31 AF XY: 0.151 AC XY: 108257 AN XY: 715420

African (AFR) AF: 0.0751 AC: 2448 AN: 32594

American (AMR) AF: 0.0672 AC: 2815 AN: 41882

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 3955 AN: 25104

East Asian (EAS) AF: 0.000482 AC: 19 AN: 39390

South Asian (SAS) AF: 0.165 AC: 13706 AN: 83248

European-Finnish (FIN) AF: 0.133 AC: 7004 AN: 52776

Middle Eastern (MID) AF: 0.183 AC: 1030 AN: 5622

European-Non Finnish (NFE) AF: 0.160 AC: 175854 AN: 1100966

Other (OTH) AF: 0.146 AC: 8673 AN: 59444

GnomAD4 genome AF: 0.124 AC: 18840 AN: 152136 Hom.: 1336 Cov.: 32 AF XY: 0.121 AC XY: 9012 AN XY: 74368

African (AFR) AF: 0.0772 AC: 3205 AN: 41524

American (AMR) AF: 0.0968 AC: 1480 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 564 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5178

South Asian (SAS) AF: 0.145 AC: 698 AN: 4822

European-Finnish (FIN) AF: 0.116 AC: 1223 AN: 10570

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11283 AN: 67962

Other (OTH) AF: 0.123 AC: 259 AN: 2114

Alfa AF: 0.152 Hom.: 598

Bravo AF: 0.117

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.7
DANN	Benign	0.75
PhyloP100		0.014
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs8192688;

hg19: chr8-82392849;