Genetic Variant FABP2:p.Asn72Asn (chr4-119320694-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -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

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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

GnomAD3 exomes

AF:

0.564

AC:

130168

AN:

230746

Hom.:

37277

AF XY:

0.558

AC XY:

69968

AN XY:

125358

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 SAS exome

AF:

0.504

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

Gnomad4 AFR exome

AF:

0.553

Gnomad4 AMR exome

AF:

0.636

Gnomad4 ASJ exome

AF:

0.635

Gnomad4 EAS exome

AF:

0.576

Gnomad4 SAS exome

AF:

0.508

Gnomad4 FIN exome

AF:

0.507

Gnomad4 NFE exome

AF:

0.570

Gnomad4 OTH exome

AF:

0.577

GnomAD4 genome

AF:

0.567

AC:

86069

AN:

151780

Hom.:

24417

Cov.:

AF XY:

0.564

AC XY:

41820

AN XY:

74150

show subpopulations

Gnomad4 AFR

AF:

0.559

Gnomad4 AMR

AF:

0.605

Gnomad4 ASJ

AF:

0.623

Gnomad4 EAS

AF:

0.629

Gnomad4 SAS

AF:

0.533

Gnomad4 FIN

AF:

0.511

Gnomad4 NFE

AF:

0.567

Gnomad4 OTH

AF:

0.600

Alfa

AF:

0.570

Hom.:

45312

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

Nov 11, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

3.1

DANN

Benign

0.28

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over