Genetic Variant FABP2:p.Asn72Asn (chr4-119320694-A-G) – 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.216T>C(p.Asn72Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 1,591,276 control chromosomes in the GnomAD database, including 257,184 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.57 ( 24417 hom., cov: 31)

Exomes 𝑓: 0.57 ( 232767 hom. )

Consequence

FABP2
NM_000134.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.367

Publications

26 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:

Genome browser will be placed here

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=-0.73).

BP6

Variant 4-119320694-A-G is Benign according to our data. Variant chr4-119320694-A-G is described in ClinVar as Benign. ClinVar VariationId is 1232917.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.367 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP2	NM_000134.4 link	c.216T>C	p.Asn72Asn	synonymous_variant	Exon 2 of 4	ENST00000274024.4	NP_000125.2	P12104

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP2	ENST00000274024.4 link	c.216T>C	p.Asn72Asn	synonymous_variant	Exon 2 of 4	1	NM_000134.4	ENSP00000274024.3		P12104

Frequencies

GnomAD3 genomes

AF:

0.567

AC:

85970

AN:

151662

Hom.:

24384

Cov.:

show subpopulations

Gnomad AFR

AF:

0.559

Gnomad AMI

AF:

0.448

Gnomad AMR

AF:

0.605

Gnomad ASJ

AF:

0.623

Gnomad EAS

AF:

0.629

Gnomad SAS

AF:

0.533

Gnomad FIN

AF:

0.511

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.567

Gnomad OTH

AF:

0.597

GnomAD2 exomes

AF:

0.564

AC:

130168

AN:

230746

AF XY:

0.558

show subpopulations

Gnomad AFR exome

AF:

0.549

Gnomad AMR exome

AF:

0.638

Gnomad ASJ exome

AF:

0.637

Gnomad EAS exome

AF:

0.633

Gnomad FIN exome

AF:

0.507

Gnomad NFE exome

AF:

0.555

Gnomad OTH exome

AF:

0.561

GnomAD4 exome

AF:

0.567

AC:

816223

AN:

1439496

Hom.:

232767

Cov.:

AF XY:

0.564

AC XY:

403847

AN XY:

716144

show subpopulations

African (AFR)

AF:

0.553

AC:

17557

AN:

31748

American (AMR)

AF:

0.636

AC:

25553

AN:

40202

Ashkenazi Jewish (ASJ)

AF:

0.635

AC:

16316

AN:

25702

East Asian (EAS)

AF:

0.576

AC:

22229

AN:

38602

South Asian (SAS)

AF:

0.508

AC:

41782

AN:

82244

European-Finnish (FIN)

AF:

0.507

AC:

26351

AN:

51962

Middle Eastern (MID)

AF:

0.547

AC:

2950

AN:

5390

European-Non Finnish (NFE)

AF:

0.570

AC:

629196

AN:

1104222

Other (OTH)

AF:

0.577

AC:

34289

AN:

59424

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

17372

34745

52117

69490

86862

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17628

35256

52884

70512

88140

<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:

0.567

AC:

86069

AN:

151780

Hom.:

24417

Cov.:

AF XY:

0.564

AC XY:

41820

AN XY:

74150

show subpopulations

African (AFR)

AF:

0.559

AC:

23156

AN:

41422

American (AMR)

AF:

0.605

AC:

9216

AN:

15226

Ashkenazi Jewish (ASJ)

AF:

0.623

AC:

2158

AN:

3466

East Asian (EAS)

AF:

0.629

AC:

3237

AN:

5148

South Asian (SAS)

AF:

0.533

AC:

2571

AN:

4820

European-Finnish (FIN)

AF:

0.511

AC:

5383

AN:

10532

Middle Eastern (MID)

AF:

0.578

AC:

170

AN:

294

European-Non Finnish (NFE)

AF:

0.567

AC:

38503

AN:

67852

Other (OTH)

AF:

0.600

AC:

1268

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1901

3801

5702

7602

9503

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

740

1480

2220

2960

3700

<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:

0.570

Hom.:

73150

Bravo

AF:

0.579

Asia WGS

AF:

0.634

AC:

2205

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Nov 11, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

3.1

(source)

DANN

Benign

0.28

PhyloP100

0.37

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over