Genetic Variant FABP2:c.241-19_241-5dupTATTATTATTATTAT (chr4-119319647-C-CATAATAATAATAATA) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_000134.4(FABP2):c.241-19_241-5dupTATTATTATTATTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0046 ( 4 hom., cov: 0)

Exomes 𝑓: 0.0011 ( 2 hom. )

Consequence

FABP2
NM_000134.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.118

Publications

3 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: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

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.241-19_241-5dupTATTATTATTATTAT		splice_region intron	N/A	NP_000125.2	P12104

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FABP2	ENST00000274024.4	TSL:1 MANE Select	c.241-5_241-4insTATTATTATTATTAT	splice_region intron	N/A	ENSP00000274024.3	P12104
ENSG00000294020	ENST00000720595.1		n.176-14681_176-14680insATAATAATAATAATA	intron	N/A
ENSG00000294020	ENST00000720596.1		n.224-14681_224-14680insATAATAATAATAATA	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00457

AC:

662

AN:

144892

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00793

Gnomad AMI

AF:

0.00563

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.000293

Gnomad EAS

AF:

0.00321

Gnomad SAS

AF:

0.00175

Gnomad FIN

AF:

0.00244

Gnomad MID

AF:

0.00329

Gnomad NFE

AF:

0.00376

Gnomad OTH

AF:

0.00204

GnomAD4 exome

AF:

0.00111

AC:

722

AN:

653048

Hom.:

Cov.:

AF XY:

0.00121

AC XY:

408

AN XY:

338254

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00433

AC:

AN:

12690

American (AMR)

AF:

0.000754

AC:

AN:

14584

Ashkenazi Jewish (ASJ)

AF:

0.000313

AC:

AN:

15976

East Asian (EAS)

AF:

0.00116

AC:

AN:

22326

South Asian (SAS)

AF:

0.000573

AC:

AN:

36666

European-Finnish (FIN)

AF:

0.000882

AC:

AN:

28332

Middle Eastern (MID)

AF:

0.000916

AC:

AN:

2184

European-Non Finnish (NFE)

AF:

0.00111

AC:

543

AN:

491048

Other (OTH)

AF:

0.00116

AC:

AN:

29242

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.389

Heterozygous variant carriers

100

134

167

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.00456

AC:

661

AN:

144904

Hom.:

Cov.:

AF XY:

0.00445

AC XY:

313

AN XY:

70288

show subpopulations

African (AFR)

AF:

0.00791

AC:

314

AN:

39680

American (AMR)

AF:

0.00300

AC:

AN:

14314

Ashkenazi Jewish (ASJ)

AF:

0.000293

AC:

AN:

3414

East Asian (EAS)

AF:

0.00302

AC:

AN:

4960

South Asian (SAS)

AF:

0.00176

AC:

AN:

4556

European-Finnish (FIN)

AF:

0.00244

AC:

AN:

8618

Middle Eastern (MID)

AF:

0.00360

AC:

AN:

278

European-Non Finnish (NFE)

AF:

0.00376

AC:

249

AN:

66224

Other (OTH)

AF:

0.00203

AC:

AN:

1972

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

122

153

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00360

Hom.:

121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.12

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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4-119319647-CATAATAATAATAATA-CATAATAATAATAATAATAATAATAATAATA

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