4-119320990-C-T

Position:

• chr4-119320990-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.68-148G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 606,770 control chromosomes in the GnomAD database, including 30,527 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.34 (8746 hom., cov: 33)
  • Exomes 𝑓: 0.30 (21781 hom.)
• Consequence: FABP2 NM_000134.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.76

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=-0.92).
• BP6: Variant 4-119320990-C-T is Benign according to our data. Variant chr4-119320990-C-T is described in ClinVar as [Benign]. Clinvar id is 1241519.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FABP2	NM_000134.4	c.68-148G>A		intron_variant		ENST00000274024.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP2	ENST00000274024.4	c.68-148G>A		intron_variant		1	NM_000134.4	P1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51038 AN: 151594 Hom.: 8729 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.341

GnomAD4 exome AF: 0.302 AC: 137388 AN: 455058 Hom.: 21781 AF XY: 0.296 AC XY: 70264 AN XY: 237624

Gnomad4 AFR exome AF: 0.366

Gnomad4 AMR exome AF: 0.306

Gnomad4 ASJ exome AF: 0.211

Gnomad4 EAS exome AF: 0.333

Gnomad4 SAS exome AF: 0.191

Gnomad4 FIN exome AF: 0.289

Gnomad4 NFE exome AF: 0.314

Gnomad4 OTH exome AF: 0.308

GnomAD4 genome AF: 0.337 AC: 51100 AN: 151712 Hom.: 8746 Cov.: 33 AF XY: 0.334 AC XY: 24763 AN XY: 74154

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.342

Alfa AF: 0.326 Hom.: 1060

Bravo AF: 0.348

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

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0080
DANN	Benign	0.36

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: rs10006259; hg19: chr4-120242145;