Genetic Variant ENSG00000294020:n.176-12064A>T (chr4-119322264-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000720595.1(ENSG00000294020):n.176-12064A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 511,312 control chromosomes in the GnomAD database, including 81,098 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.57 ( 24212 hom., cov: 32)

Exomes 𝑓: 0.56 ( 56886 hom. )

Consequence

ENSG00000294020
ENST00000720595.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.158

Publications

4 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 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.-162T>A		upstream_gene	N/A	NP_000125.2	P12104

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000294020	ENST00000720595.1	n.176-12064A>T	intron	N/A
ENSG00000294020	ENST00000720596.1	n.224-12064A>T	intron	N/A
ENSG00000294020	ENST00000720597.1	n.238-12064A>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.565

AC:

85594

AN:

151382

Hom.:

24178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.557

Gnomad AMI

AF:

0.447

Gnomad AMR

AF:

0.603

Gnomad ASJ

AF:

0.620

Gnomad EAS

AF:

0.627

Gnomad SAS

AF:

0.532

Gnomad FIN

AF:

0.509

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.567

Gnomad OTH

AF:

0.593

GnomAD4 exome

AF:

0.558

AC:

200779

AN:

359812

Hom.:

56886

Cov.:

AF XY:

0.555

AC XY:

105194

AN XY:

189492

show subpopulations

African (AFR)

AF:

0.560

AC:

5266

AN:

9396

American (AMR)

AF:

0.633

AC:

8677

AN:

13708

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

7250

AN:

11494

East Asian (EAS)

AF:

0.557

AC:

14887

AN:

26730

South Asian (SAS)

AF:

0.505

AC:

11420

AN:

22608

European-Finnish (FIN)

AF:

0.500

AC:

15284

AN:

30544

Middle Eastern (MID)

AF:

0.585

AC:

1808

AN:

3090

European-Non Finnish (NFE)

AF:

0.560

AC:

123829

AN:

220956

Other (OTH)

AF:

0.581

AC:

12358

AN:

21286

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

4197

8394

12590

16787

20984

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

678

1356

2034

2712

3390

<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:

0.566

AC:

85693

AN:

151500

Hom.:

24212

Cov.:

AF XY:

0.562

AC XY:

41634

AN XY:

74028

show subpopulations

African (AFR)

AF:

0.558

AC:

23030

AN:

41304

American (AMR)

AF:

0.603

AC:

9170

AN:

15210

Ashkenazi Jewish (ASJ)

AF:

0.620

AC:

2140

AN:

3452

East Asian (EAS)

AF:

0.627

AC:

3219

AN:

5138

South Asian (SAS)

AF:

0.533

AC:

2568

AN:

4822

European-Finnish (FIN)

AF:

0.509

AC:

5355

AN:

10514

Middle Eastern (MID)

AF:

0.569

AC:

165

AN:

290

European-Non Finnish (NFE)

AF:

0.566

AC:

38390

AN:

67768

Other (OTH)

AF:

0.597

AC:

1250

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1938

3876

5813

7751

9689

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

736

1472

2208

2944

3680

<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

Bravo

AF:

0.578

Asia WGS

AF:

0.633

AC:

2198

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.8

(source)

DANN

Benign

0.62

PhyloP100

-0.16

PromoterAI

0.0036

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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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