chr4-119318723-G-A

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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	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

Gnomad4 AFR exome AF: 0.516

Gnomad4 AMR exome AF: 0.343

Gnomad4 ASJ exome AF: 0.279

Gnomad4 EAS exome AF: 0.369

Gnomad4 SAS exome AF: 0.282

Gnomad4 FIN exome AF: 0.443

Gnomad4 NFE exome AF: 0.440

Gnomad4 OTH exome AF: 0.413

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

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.458

Alfa AF: 0.455 Hom.: 32531

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs11724758; hg19: chr4-120239878;