rs5861422

Positions:

• chr4-119322181-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The 4-119322181-TA-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.57 (24369 hom., cov: 0)
  • Exomes 𝑓: 0.58 (158253 hom.)
• Consequence: FABP2 NM_000134.4 upstream_gene
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.198

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 -10 ACMG points.

• BP6: Variant 4-119322181-TA-T is Benign according to our data. Variant chr4-119322181-TA-T is described in ClinVar as [Benign]. Clinvar id is 1229473.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FABP2	NM_000134.4			upstream_gene_variant		ENST00000274024.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP2	ENST00000274024.4			upstream_gene_variant		1	NM_000134.4	P1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85873 AN: 151634 Hom.: 24336 Cov.: 0

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.594

GnomAD4 exome AF: 0.576 AC: 544767 AN: 946078 Hom.: 158253 Cov.: 0 AF XY: 0.572 AC XY: 278338 AN XY: 486990

Gnomad4 AFR exome AF: 0.566

Gnomad4 AMR exome AF: 0.649

Gnomad4 ASJ exome AF: 0.636

Gnomad4 EAS exome AF: 0.576

Gnomad4 SAS exome AF: 0.520

Gnomad4 FIN exome AF: 0.509

Gnomad4 NFE exome AF: 0.581

Gnomad4 OTH exome AF: 0.586

GnomAD4 genome AF: 0.567 AC: 85971 AN: 151752 Hom.: 24369 Cov.: 0 AF XY: 0.563 AC XY: 41767 AN XY: 74154

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.598

Alfa AF: 0.409 Hom.: 981

Bravo AF: 0.579

Asia WGS AF: 0.634 AC: 2204 AN: 3478

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

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: rs5861422; hg19: chr4-120243336;