Genetic Variant FABP2:c.241-10_241-5delTATTAT (chr4-119319647-CATAATA-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000134.4(FABP2):c.241-10_241-5delTATTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00423 in 797,376 control chromosomes in the GnomAD database, including 98 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.015 ( 56 hom., cov: 0)

Exomes 𝑓: 0.0019 ( 42 hom. )

Consequence

FABP2
NM_000134.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.17

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.061 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.241-10_241-5delTATTAT		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.241-10_241-5delTATTAT	splice_region intron	N/A	ENSP00000274024.3	P12104
ENSG00000294020	ENST00000720595.1		n.176-14680_176-14675delATAATA	intron	N/A
ENSG00000294020	ENST00000720596.1		n.224-14680_224-14675delATAATA	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0148

AC:

2142

AN:

144894

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0504

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00636

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000655

Gnomad FIN

AF:

0.000116

Gnomad MID

AF:

0.00987

Gnomad NFE

AF:

0.000453

Gnomad OTH

AF:

0.00817

GnomAD2 exomes

AF:

0.00253

AC:

190

AN:

75038

AF XY:

0.00185

show subpopulations

Gnomad AFR exome

AF:

0.0427

Gnomad AMR exome

AF:

0.00259

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000379

Gnomad FIN exome

AF:

0.000338

Gnomad NFE exome

AF:

0.000240

Gnomad OTH exome

AF:

0.00186

GnomAD4 exome

AF:

0.00189

AC:

1232

AN:

652470

Hom.:

AF XY:

0.00156

AC XY:

527

AN XY:

337970

show subpopulations

African (AFR)

AF:

0.0647

AC:

816

AN:

12612

American (AMR)

AF:

0.00377

AC:

AN:

14578

Ashkenazi Jewish (ASJ)

AF:

0.000251

AC:

AN:

15946

East Asian (EAS)

AF:

0.000180

AC:

AN:

22250

South Asian (SAS)

AF:

0.000792

AC:

AN:

36618

European-Finnish (FIN)

AF:

0.000318

AC:

AN:

28310

Middle Eastern (MID)

AF:

0.00321

AC:

AN:

2180

European-Non Finnish (NFE)

AF:

0.000363

AC:

178

AN:

490766

Other (OTH)

AF:

0.00445

AC:

130

AN:

29210

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.545

Heterozygous variant carriers

122

163

204

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

130

<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:

0.0148

AC:

2142

AN:

144906

Hom.:

Cov.:

AF XY:

0.0146

AC XY:

1023

AN XY:

70284

show subpopulations

African (AFR)

AF:

0.0504

AC:

1999

AN:

39676

American (AMR)

AF:

0.00629

AC:

AN:

14318

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3414

East Asian (EAS)

AF:

0.00

AC:

AN:

4960

South Asian (SAS)

AF:

0.000658

AC:

AN:

4556

European-Finnish (FIN)

AF:

0.000116

AC:

AN:

8618

Middle Eastern (MID)

AF:

0.0108

AC:

AN:

278

European-Non Finnish (NFE)

AF:

0.000453

AC:

AN:

66228

Other (OTH)

AF:

0.00812

AC:

AN:

1970

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

187

280

374

467

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<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:

0.00

Hom.:

121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.2

Mutation Taster

=98/2

polymorphism

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

4-119319647-CATAATAATAATAATA-CATAATAATA

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