4-119320519-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000134.4(FABP2):c.240+151G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 562,374 control chromosomes in the GnomAD database, including 28,635 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.34 (8816 hom., cov: 32)
  • Exomes 𝑓: 0.30 (19819 hom.)
• Consequence: FABP2 NM_000134.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.51

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 4-119320519-C-T is Benign according to our data. Variant chr4-119320519-C-T is described in ClinVar as [Benign]. Clinvar id is 1289789.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FABP2	NM_000134.4	c.240+151G>A		intron_variant		ENST00000274024.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP2	ENST00000274024.4	c.240+151G>A		intron_variant		1	NM_000134.4	P1

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51166 AN: 151588 Hom.: 8800 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.343

GnomAD4 exome AF: 0.304 AC: 124979 AN: 410670 Hom.: 19819 AF XY: 0.298 AC XY: 64541 AN XY: 216706

Gnomad4 AFR exome AF: 0.375

Gnomad4 AMR exome AF: 0.312

Gnomad4 ASJ exome AF: 0.213

Gnomad4 EAS exome AF: 0.337

Gnomad4 SAS exome AF: 0.197

Gnomad4 FIN exome AF: 0.289

Gnomad4 NFE exome AF: 0.317

Gnomad4 OTH exome AF: 0.312

GnomAD4 genome AF: 0.338 AC: 51226 AN: 151704 Hom.: 8816 Cov.: 32 AF XY: 0.335 AC XY: 24824 AN XY: 74114

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.344

Alfa AF: 0.326 Hom.: 1063

Bravo AF: 0.348

Asia WGS AF: 0.294 AC: 1021 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.1
Dann	Benign	0.33

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: rs10003567; hg19: chr4-120241674; COSMIC: COSV56789115;