Genetic Variant FABP2:p.Val119Val (chr4-119319083-T-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000134.4(FABP2):c.357A>G(p.Val119Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 1,590,014 control chromosomes in the GnomAD database, including 86,219 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 8810 hom., cov: 32)

Exomes 𝑓: 0.32 ( 77409 hom. )

Consequence

FABP2
NM_000134.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.09

Publications

24 publications found

Variant links:

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]

FABP2 links:

ENSG00000294020 (HGNC:):

ENSG00000294020 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 4-119319083-T-C is Benign according to our data. Variant chr4-119319083-T-C is described in ClinVar as Benign. ClinVar VariationId is 1259953.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000134.4. 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.357A>G	p.Val119Val	synonymous	Exon 4 of 4	NP_000125.2	P12104

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FABP2	ENST00000274024.4	TSL:1 MANE Select	c.357A>G	p.Val119Val	synonymous	Exon 4 of 4	ENSP00000274024.3	P12104
ENSG00000294020	ENST00000720595.1		n.176-15245T>C		intron	N/A
ENSG00000294020	ENST00000720596.1		n.224-15245T>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51157

AN:

151648

Hom.:

8793

Cov.:

show subpopulations

Gnomad AFR

AF:

0.385

Gnomad AMI

AF:

0.343

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.387

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.341

GnomAD2 exomes

AF:

0.309

AC:

73543

AN:

237654

AF XY:

0.302

show subpopulations

Gnomad AFR exome

AF:

0.382

Gnomad AMR exome

AF:

0.307

Gnomad ASJ exome

AF:

0.212

Gnomad EAS exome

AF:

0.395

Gnomad FIN exome

AF:

0.303

Gnomad NFE exome

AF:

0.324

Gnomad OTH exome

AF:

0.292

GnomAD4 exome

AF:

0.324

AC:

465417

AN:

1438248

Hom.:

77409

Cov.:

AF XY:

0.319

AC XY:

228406

AN XY:

716138

show subpopulations

African (AFR)

AF:

0.378

AC:

12194

AN:

32294

American (AMR)

AF:

0.310

AC:

12775

AN:

41210

Ashkenazi Jewish (ASJ)

AF:

0.215

AC:

5560

AN:

25834

East Asian (EAS)

AF:

0.356

AC:

13719

AN:

38590

South Asian (SAS)

AF:

0.206

AC:

17246

AN:

83668

European-Finnish (FIN)

AF:

0.298

AC:

15825

AN:

53156

Middle Eastern (MID)

AF:

0.289

AC:

1643

AN:

5678

European-Non Finnish (NFE)

AF:

0.335

AC:

367813

AN:

1098458

Other (OTH)

AF:

0.314

AC:

18642

AN:

59360

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

12594

25188

37781

50375

62969

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11876

23752

35628

47504

59380

<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:

0.337

AC:

51219

AN:

151766

Hom.:

8810

Cov.:

AF XY:

0.335

AC XY:

24814

AN XY:

74166

show subpopulations

African (AFR)

AF:

0.385

AC:

15965

AN:

41422

American (AMR)

AF:

0.309

AC:

4704

AN:

15218

Ashkenazi Jewish (ASJ)

AF:

0.205

AC:

710

AN:

3468

East Asian (EAS)

AF:

0.388

AC:

1995

AN:

5148

South Asian (SAS)

AF:

0.209

AC:

1011

AN:

4830

European-Finnish (FIN)

AF:

0.295

AC:

3105

AN:

10512

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.333

AC:

22606

AN:

67862

Other (OTH)

AF:

0.342

AC:

719

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1717

3433

5150

6866

8583

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

512

1024

1536

2048

2560

<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:

0.333

Hom.:

13191

Bravo

AF:

0.348

Asia WGS

AF:

0.294

AC:

1020

AN:

3472

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.083

(source)

DANN

Benign

0.44

PhyloP100

-2.1

Mutation Taster

=100/0

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