Genetic Variant FABP2:c.241-7_241-5delTAT (chr4-119319647-CATA-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000134.4(FABP2):c.241-7_241-5delTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 787,412 control chromosomes in the GnomAD database, including 1,250 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.067 ( 971 hom., cov: 0)

Exomes 𝑓: 0.014 ( 279 hom. )

Consequence

FABP2
NM_000134.4 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.189

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 -10 ACMG points.

BP6

Variant 4-119319647-CATA-C is Benign according to our data. Variant chr4-119319647-CATA-C is described in ClinVar as Benign. ClinVar VariationId is 1250553.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 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.241-7_241-5delTAT		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.241-7_241-5delTAT	splice_region intron	N/A	ENSP00000274024.3	P12104
ENSG00000294020	ENST00000720595.1		n.176-14680_176-14678delATA	intron	N/A
ENSG00000294020	ENST00000720596.1		n.224-14680_224-14678delATA	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0669

AC:

9689

AN:

144844

Hom.:

969

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0296

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0579

Gnomad SAS

AF:

0.0212

Gnomad FIN

AF:

0.000581

Gnomad MID

AF:

0.0132

Gnomad NFE

AF:

0.00181

Gnomad OTH

AF:

0.0541

GnomAD2 exomes

AF:

0.0108

AC:

808

AN:

75038

AF XY:

0.0102

show subpopulations

Gnomad AFR exome

AF:

0.0924

Gnomad AMR exome

AF:

0.0105

Gnomad ASJ exome

AF:

0.00431

Gnomad EAS exome

AF:

0.0246

Gnomad FIN exome

AF:

0.00406

Gnomad NFE exome

AF:

0.00307

Gnomad OTH exome

AF:

0.00868

GnomAD4 exome

AF:

0.0142

AC:

9141

AN:

642556

Hom.:

279

AF XY:

0.0136

AC XY:

4533

AN XY:

332516

show subpopulations

African (AFR)

AF:

0.210

AC:

2640

AN:

12580

American (AMR)

AF:

0.0201

AC:

288

AN:

14324

Ashkenazi Jewish (ASJ)

AF:

0.00800

AC:

123

AN:

15376

East Asian (EAS)

AF:

0.0695

AC:

1520

AN:

21884

South Asian (SAS)

AF:

0.0184

AC:

666

AN:

36110

European-Finnish (FIN)

AF:

0.00708

AC:

197

AN:

27818

Middle Eastern (MID)

AF:

0.0215

AC:

AN:

2138

European-Non Finnish (NFE)

AF:

0.00594

AC:

2873

AN:

483680

Other (OTH)

AF:

0.0275

AC:

788

AN:

28646

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

Heterozygous variant carriers

366

732

1098

1464

1830

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

256

384

512

640

<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:

0.0670

AC:

9708

AN:

144856

Hom.:

971

Cov.:

AF XY:

0.0655

AC XY:

4600

AN XY:

70266

show subpopulations

African (AFR)

AF:

0.219

AC:

8668

AN:

39660

American (AMR)

AF:

0.0296

AC:

423

AN:

14310

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3414

East Asian (EAS)

AF:

0.0581

AC:

288

AN:

4956

South Asian (SAS)

AF:

0.0206

AC:

AN:

4554

European-Finnish (FIN)

AF:

0.000581

AC:

AN:

8608

Middle Eastern (MID)

AF:

0.0144

AC:

AN:

278

European-Non Finnish (NFE)

AF:

0.00181

AC:

120

AN:

66218

Other (OTH)

AF:

0.0538

AC:

106

AN:

1970

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

349

699

1048

1398

1747

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

204

306

408

510

<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:

0.000533

Hom.:

121

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.19

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

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-CATAATAATAATA

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