rs1546505

Variant names:

• chr4-119320069-A-G
• rs1546505
• NM_000134.4:c.241-426T>C

Variant summary

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

The NM_000134.4(FABP2):​c.241-426T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,866 control chromosomes in the GnomAD database, including 5,582 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 0.27 (5582 hom., cov: 32)
• Consequence: FABP2 NM_000134.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73
• Publications: 13 publications found

Genes affected

FABP2 (HGNC:3556): (fatty acid binding protein 2) The protein encoded by this gene is an intracellular fatty acid-binding protein that participates in the uptake, intracellular metabolism, and transport of long-chain fatty acids. The encoded protein is also involved in the modulation of cell growth and proliferation. This protein binds saturated long-chain fatty acids with high affinity, and may act as a lipid sensor to maintain energy homeostasis. [provided by RefSeq, Aug 2017]

ENSG00000294020 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP2	NM_000134.4	c.241-426T>C		intron_variant	Intron 2 of 3	ENST00000274024.4	NP_000125.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP2	ENST00000274024.4	c.241-426T>C		intron_variant	Intron 2 of 3	1	NM_000134.4	ENSP00000274024.3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40689 AN: 151748 Hom.: 5581 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.268 AC: 40709 AN: 151866 Hom.: 5582 Cov.: 32 AF XY: 0.265 AC XY: 19678 AN XY: 74210

African (AFR) AF: 0.225 AC: 9337 AN: 41478

American (AMR) AF: 0.264 AC: 4028 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1965 AN: 5148

South Asian (SAS) AF: 0.176 AC: 851 AN: 4824

European-Finnish (FIN) AF: 0.259 AC: 2732 AN: 10560

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20233 AN: 67836

Other (OTH) AF: 0.282 AC: 593 AN: 2104

Alfa AF: 0.270 Hom.: 975

Bravo AF: 0.274

Asia WGS AF: 0.252 AC: 875 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.7
DANN	Benign	0.87
PhyloP100		1.7
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: rs1546505; hg19: chr4-120241224;