rs16909192

Variant names:

• chr8-81478608-A-C
• rs16909192
• NM_001442.3:c.*257T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000256104.5(FABP4):​c.*257T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 368,384 control chromosomes in the GnomAD database, including 4,193 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 0.13 (1405 hom., cov: 32)
  • Exomes 𝑓: 0.14 (2788 hom.)
• Consequence: FABP4 ENST00000256104.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.663
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000256104.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP4	NM_001442.3	MANE Select	c.*257T>G		3_prime_UTR	Exon 4 of 4	NP_001433.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP4	ENST00000256104.5	TSL:1 MANE Select	c.*257T>G		3_prime_UTR	Exon 4 of 4	ENSP00000256104.4
	ENSG00000253374	ENST00000524085.2	TSL:5	n.299-19309A>C		intron	N/A
	ENSG00000253374	ENST00000832857.1		n.326+38515A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19271 AN: 152080 Hom.: 1402 Cov.: 32

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0978

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.144 AC: 31176 AN: 216186 Hom.: 2788 Cov.: 0 AF XY: 0.148 AC XY: 16359 AN XY: 110872

African (AFR) AF: 0.0697 AC: 484 AN: 6944

American (AMR) AF: 0.0812 AC: 718 AN: 8844

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 1270 AN: 7638

East Asian (EAS) AF: 0.000383 AC: 7 AN: 18292

South Asian (SAS) AF: 0.170 AC: 1495 AN: 8784

European-Finnish (FIN) AF: 0.135 AC: 2101 AN: 15620

Middle Eastern (MID) AF: 0.171 AC: 183 AN: 1070

European-Non Finnish (NFE) AF: 0.169 AC: 22851 AN: 135178

Other (OTH) AF: 0.150 AC: 2067 AN: 13816

GnomAD4 genome AF: 0.127 AC: 19283 AN: 152198 Hom.: 1405 Cov.: 32 AF XY: 0.124 AC XY: 9194 AN XY: 74406

African (AFR) AF: 0.0786 AC: 3267 AN: 41546

American (AMR) AF: 0.0978 AC: 1493 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3472

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5192

South Asian (SAS) AF: 0.147 AC: 710 AN: 4822

European-Finnish (FIN) AF: 0.113 AC: 1197 AN: 10590

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

European-Non Finnish (NFE) AF: 0.171 AC: 11618 AN: 67984

Other (OTH) AF: 0.128 AC: 270 AN: 2116

Alfa AF: 0.161 Hom.: 942

Bravo AF: 0.120

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.7
DANN	Benign	0.75
PhyloP100		0.66
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: rs16909192; hg19: chr8-82390843;