NM_001442.3:c.247-124A>G

Variant names:

• chr8-81479639-T-C
• rs2305319
• NM_001442.3:c.247-124A>G

Variant summary

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

The NM_001442.3(FABP4):​c.247-124A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 607,306 control chromosomes in the GnomAD database, including 7,964 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 (1874 hom., cov: 32)
  • Exomes 𝑓: 0.16 (6090 hom.)
• Consequence: FABP4 NM_001442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.672
• Publications: 2 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=-0.79).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP4	NM_001442.3	MANE Select	c.247-124A>G		intron	N/A	NP_001433.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP4	ENST00000256104.5	TSL:1 MANE Select	c.247-124A>G		intron	N/A	ENSP00000256104.4
	FABP4	ENST00000521734.1	TSL:2	n.332A>G		non_coding_transcript_exon	Exon 1 of 2
	FABP4	ENST00000518669.5	TSL:3	n.182-124A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23451 AN: 151970 Hom.: 1867 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0677

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.148

GnomAD4 exome AF: 0.156 AC: 70901 AN: 455218 Hom.: 6090 Cov.: 6 AF XY: 0.159 AC XY: 38126 AN XY: 240198

African (AFR) AF: 0.158 AC: 1939 AN: 12284

American (AMR) AF: 0.144 AC: 2465 AN: 17106

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 2168 AN: 13286

East Asian (EAS) AF: 0.0618 AC: 1896 AN: 30664

South Asian (SAS) AF: 0.191 AC: 6988 AN: 36492

European-Finnish (FIN) AF: 0.133 AC: 4794 AN: 36030

Middle Eastern (MID) AF: 0.206 AC: 666 AN: 3238

European-Non Finnish (NFE) AF: 0.163 AC: 45842 AN: 280680

Other (OTH) AF: 0.163 AC: 4143 AN: 25438

GnomAD4 genome AF: 0.154 AC: 23491 AN: 152088 Hom.: 1874 Cov.: 32 AF XY: 0.152 AC XY: 11286 AN XY: 74352

African (AFR) AF: 0.157 AC: 6504 AN: 41468

American (AMR) AF: 0.142 AC: 2173 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3468

East Asian (EAS) AF: 0.0678 AC: 352 AN: 5190

South Asian (SAS) AF: 0.173 AC: 831 AN: 4816

European-Finnish (FIN) AF: 0.116 AC: 1228 AN: 10582

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

European-Non Finnish (NFE) AF: 0.167 AC: 11365 AN: 67986

Other (OTH) AF: 0.150 AC: 317 AN: 2108

Alfa AF: 0.167 Hom.: 260

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	-0.79
CADD	Benign	8.7
DANN	Benign	0.72
PhyloP100		0.67
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: rs2305319; hg19: chr8-82391874;