dbSNP rs5861423: ENSG00000294020:n.176-12094_176-12093insCTACT (chr4-119322234-A-ACTACT) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.155

Publications

2 publications found

Variant links:

Genes affected

ENSG00000294020 (HGNC:):

ENSG00000294020 links:

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]

FABP2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Selected	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

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
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.:

show subpopulations

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.:

AF XY:

0.566

AC XY:

141477

AN XY:

250084

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.531

Heterozygous variant carriers

5386

10773

16159

21546

26932

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1074

2148

3222

4296

5370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.565

AC:

85618

AN:

151424

Hom.:

24189

Cov.:

AF XY:

0.562

AC XY:

41569

AN XY:

73946

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1901

3802

5702

7603

9504

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

734

1468

2202

2936

3670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.357

Hom.:

629

Asia WGS

AF:

0.633

AC:

2203

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.15

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over