4-119318976-T-C

Position:

• chr4-119318976-T-C

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.*65A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 1,262,452 control chromosomes in the GnomAD database, including 65,042 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.34 (8812 hom., cov: 31)
  • Exomes 𝑓: 0.31 (56230 hom.)
• Consequence: FABP2 NM_000134.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.735

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=-0.91).
• BP6: Variant 4-119318976-T-C is Benign according to our data. Variant chr4-119318976-T-C is described in ClinVar as [Benign]. Clinvar id is 1236503.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.*65A>G		3_prime_UTR_variant	4/4	ENST00000274024.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP2	ENST00000274024.4	c.*65A>G		3_prime_UTR_variant	4/4	1	NM_000134.4	P1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51158 AN: 151636 Hom.: 8795 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.341

GnomAD4 exome AF: 0.313 AC: 347849 AN: 1110700 Hom.: 56230 Cov.: 14 AF XY: 0.309 AC XY: 175145 AN XY: 566726

Gnomad4 AFR exome AF: 0.369

Gnomad4 AMR exome AF: 0.304

Gnomad4 ASJ exome AF: 0.212

Gnomad4 EAS exome AF: 0.345

Gnomad4 SAS exome AF: 0.201

Gnomad4 FIN exome AF: 0.297

Gnomad4 NFE exome AF: 0.325

Gnomad4 OTH exome AF: 0.306

GnomAD4 genome AF: 0.338 AC: 51219 AN: 151752 Hom.: 8812 Cov.: 31 AF XY: 0.335 AC XY: 24811 AN XY: 74156

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.343

Alfa AF: 0.331 Hom.: 3331

Bravo AF: 0.348

Asia WGS AF: 0.295 AC: 1019 AN: 3456

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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2964; hg19: chr4-120240131; COSMIC: COSV56788270;