rs5861423

Variant names:

• chr4-119322234-A-ACTACT
• rs5861423
• ENST00000720595.1:n.176-12094_176-12093insCTACT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000720595.1(ENSG00000294020):​n.176-12094_176-12093insCTACT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.57 (24189 hom., cov: 0)
  • Exomes 𝑓: 0.57 (77399 hom.)
• Consequence: ENSG00000294020 ENST00000720595.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.155
• Publications: 2 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 -10 ACMG points.

• BP6: Variant 4-119322234-A-ACTACT is Benign according to our data. Variant chr4-119322234-A-ACTACT is described in ClinVar as Benign. ClinVar VariationId is 1261472.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720595.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP2	NM_000134.4	MANE Select	c.-133_-132insAGTAG		upstream_gene	N/A	NP_000125.2	P12104

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294020	ENST00000720595.1		n.176-12094_176-12093insCTACT		intron	N/A
	ENSG00000294020	ENST00000720596.1		n.224-12094_224-12093insCTACT		intron	N/A
	ENSG00000294020	ENST00000720597.1		n.238-12094_238-12093insCTACT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85520 AN: 151306 Hom.: 24156 Cov.: 0

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.595

GnomAD4 exome AF: 0.569 AC: 266077 AN: 468010 Hom.: 77399 Cov.: 5 AF XY: 0.566 AC XY: 141477 AN XY: 250084

African (AFR) AF: 0.570 AC: 7093 AN: 12450

American (AMR) AF: 0.654 AC: 14254 AN: 21800

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 8531 AN: 13362

East Asian (EAS) AF: 0.572 AC: 18425 AN: 32192

South Asian (SAS) AF: 0.541 AC: 20620 AN: 38090

European-Finnish (FIN) AF: 0.508 AC: 21475 AN: 42282

Middle Eastern (MID) AF: 0.581 AC: 2037 AN: 3508

European-Non Finnish (NFE) AF: 0.569 AC: 158462 AN: 278390

Other (OTH) AF: 0.585 AC: 15180 AN: 25936

GnomAD4 genome AF: 0.565 AC: 85618 AN: 151424 Hom.: 24189 Cov.: 0 AF XY: 0.562 AC XY: 41569 AN XY: 73946

African (AFR) AF: 0.556 AC: 22939 AN: 41262

American (AMR) AF: 0.604 AC: 9184 AN: 15214

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

East Asian (EAS) AF: 0.627 AC: 3209 AN: 5118

South Asian (SAS) AF: 0.533 AC: 2567 AN: 4812

European-Finnish (FIN) AF: 0.509 AC: 5340 AN: 10484

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

European-Non Finnish (NFE) AF: 0.567 AC: 38404 AN: 67782

Other (OTH) AF: 0.599 AC: 1258 AN: 2100

Alfa AF: 0.357 Hom.: 629

Asia WGS AF: 0.633 AC: 2203 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.15
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5861423;

hg19: chr4-120243389;

COSMIC: COSV56788126;