rs11724758

Variant names:

• chr4-119318723-G-A
• rs11724758
• NM_000134.4:c.*318C>T

Variant summary

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

The NM_000134.4(FABP2):​c.*318C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 241,526 control chromosomes in the GnomAD database, including 24,797 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 0.47 (16988 hom., cov: 32)
  • Exomes 𝑓: 0.41 (7809 hom.)
• Consequence: FABP2 NM_000134.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 31 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP2	NM_000134.4	c.*318C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000274024.4	NP_000125.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP2	ENST00000274024.4	c.*318C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_000134.4	ENSP00000274024.3

Frequencies

GnomAD3 genomes AF: 0.468 AC: 70959 AN: 151618 Hom.: 16965 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.458

GnomAD4 exome AF: 0.409 AC: 36681 AN: 89790 Hom.: 7809 Cov.: 0 AF XY: 0.398 AC XY: 19466 AN XY: 48924

African (AFR) AF: 0.516 AC: 751 AN: 1456

American (AMR) AF: 0.343 AC: 534 AN: 1556

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 780 AN: 2792

East Asian (EAS) AF: 0.369 AC: 1160 AN: 3142

South Asian (SAS) AF: 0.282 AC: 3505 AN: 12428

European-Finnish (FIN) AF: 0.443 AC: 2113 AN: 4774

Middle Eastern (MID) AF: 0.382 AC: 166 AN: 434

European-Non Finnish (NFE) AF: 0.440 AC: 25438 AN: 57800

Other (OTH) AF: 0.413 AC: 2234 AN: 5408

GnomAD4 genome AF: 0.468 AC: 71032 AN: 151736 Hom.: 16988 Cov.: 32 AF XY: 0.463 AC XY: 34342 AN XY: 74142

African (AFR) AF: 0.542 AC: 22428 AN: 41360

American (AMR) AF: 0.394 AC: 6002 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 997 AN: 3468

East Asian (EAS) AF: 0.426 AC: 2202 AN: 5170

South Asian (SAS) AF: 0.290 AC: 1396 AN: 4818

European-Finnish (FIN) AF: 0.454 AC: 4777 AN: 10532

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.468 AC: 31745 AN: 67858

Other (OTH) AF: 0.458 AC: 966 AN: 2108

Alfa AF: 0.460 Hom.: 51645

Bravo AF: 0.474

Asia WGS AF: 0.356 AC: 1238 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		-0.046
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: rs11724758; hg19: chr4-120239878;