Genetic Variant FABP2:c.*252G>A (chr4-119318789-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000134.4(FABP2):c.*252G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 357,654 control chromosomes in the GnomAD database, including 17,442 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8082 hom., cov: 32)

Exomes 𝑓: 0.30 ( 9360 hom. )

Consequence

FABP2
NM_000134.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.107

Publications

15 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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 4-119318789-C-T is Benign according to our data. Variant chr4-119318789-C-T is described in ClinVar as Benign. ClinVar VariationId is 1226605.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 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.*252G>A		3_prime_UTR	Exon 4 of 4	NP_000125.2	P12104

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FABP2	ENST00000274024.4	TSL:1 MANE Select	c.*252G>A	3_prime_UTR	Exon 4 of 4	ENSP00000274024.3	P12104
ENSG00000294020	ENST00000720595.1		n.176-15539C>T	intron	N/A
ENSG00000294020	ENST00000720596.1		n.224-15539C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49110

AN:

151772

Hom.:

8076

Cov.:

show subpopulations

Gnomad AFR

AF:

0.335

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.304

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.389

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.298

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.333

GnomAD4 exome

AF:

0.295

AC:

60750

AN:

205764

Hom.:

9360

Cov.:

AF XY:

0.290

AC XY:

31600

AN XY:

108984

show subpopulations

African (AFR)

AF:

0.311

AC:

1504

AN:

4840

American (AMR)

AF:

0.297

AC:

1520

AN:

5110

Ashkenazi Jewish (ASJ)

AF:

0.205

AC:

1441

AN:

7034

East Asian (EAS)

AF:

0.328

AC:

4688

AN:

14290

South Asian (SAS)

AF:

0.189

AC:

2850

AN:

15062

European-Finnish (FIN)

AF:

0.279

AC:

4419

AN:

15842

Middle Eastern (MID)

AF:

0.255

AC:

255

AN:

1000

European-Non Finnish (NFE)

AF:

0.310

AC:

40234

AN:

129858

Other (OTH)

AF:

0.302

AC:

3839

AN:

12728

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

2016

4031

6047

8062

10078

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

134

268

402

536

670

<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:

0.324

AC:

49144

AN:

151890

Hom.:

8082

Cov.:

AF XY:

0.321

AC XY:

23822

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.335

AC:

13892

AN:

41418

American (AMR)

AF:

0.304

AC:

4631

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.205

AC:

712

AN:

3470

East Asian (EAS)

AF:

0.389

AC:

2010

AN:

5168

South Asian (SAS)

AF:

0.209

AC:

1006

AN:

4808

European-Finnish (FIN)

AF:

0.298

AC:

3146

AN:

10544

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.333

AC:

22635

AN:

67928

Other (OTH)

AF:

0.335

AC:

707

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1748

3497

5245

6994

8742

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

498

996

1494

1992

2490

<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:

0.327

Hom.:

17809

Bravo

AF:

0.330

Asia WGS

AF:

0.292

AC:

1017

AN:

3478

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

-0.85

CADD

Benign

1.9

(source)

DANN

Benign

0.68

PhyloP100

0.11

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