chr4-119322181-TA-T

Variant names:

• chr4-119322181-TA-T
• rs5861422
• ENST00000720595.1:n.176-12146delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000720595.1(ENSG00000294020):​n.176-12146delA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.57 (24369 hom., cov: 0)
  • Exomes 𝑓: 0.58 (158253 hom.)
• Consequence: ENSG00000294020 ENST00000720595.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.198
• Publications: 5 publications found

Genes affected

ENSG00000294020 (HGNC:):

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

Our verdict: Benign. The variant received -8 ACMG points.

• 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 rank	MANE	Protein	UniProt
FABP2	NM_000134.4	c.-80delT		upstream_gene_variant		ENST00000274024.4	NP_000125.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP2	ENST00000274024.4	c.-80delT		upstream_gene_variant		1	NM_000134.4	ENSP00000274024.3

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

African (AFR) AF: 0.566 AC: 12322 AN: 21754

American (AMR) AF: 0.649 AC: 18618 AN: 28694

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 12284 AN: 19302

East Asian (EAS) AF: 0.576 AC: 20701 AN: 35910

South Asian (SAS) AF: 0.520 AC: 32451 AN: 62448

European-Finnish (FIN) AF: 0.509 AC: 25431 AN: 49974

Middle Eastern (MID) AF: 0.569 AC: 2613 AN: 4592

European-Non Finnish (NFE) AF: 0.581 AC: 395545 AN: 681070

Other (OTH) AF: 0.586 AC: 24802 AN: 42334

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

African (AFR) AF: 0.558 AC: 23113 AN: 41404

American (AMR) AF: 0.605 AC: 9202 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2147 AN: 3458

East Asian (EAS) AF: 0.629 AC: 3231 AN: 5134

South Asian (SAS) AF: 0.533 AC: 2564 AN: 4814

European-Finnish (FIN) AF: 0.510 AC: 5374 AN: 10532

Middle Eastern (MID) AF: 0.579 AC: 168 AN: 290

European-Non Finnish (NFE) AF: 0.567 AC: 38508 AN: 67892

Other (OTH) AF: 0.598 AC: 1257 AN: 2102

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

Nov 11, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.20
Mutation Taster		=201/99	polymorphism

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

Other links and lift over

dbSNP: rs5861422; hg19: chr4-120243336;