Genetic Variant FABP2:c.241-7_241-5dupTAT (chr4-119319647-C-CATA) – 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_241-5dupTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 966 hom., cov: 0)

Exomes 𝑓: 0.088 ( 1606 hom. )

Consequence

FABP2
NM_000134.4 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_000134.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 4-119319647-C-CATA is Benign according to our data. Variant chr4-119319647-C-CATA is described in ClinVar as Benign. ClinVar VariationId is 1248668.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 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_241-5dupTAT		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_241-4insTAT	splice_region intron	N/A	ENSP00000274024.3	P12104
ENSG00000294020	ENST00000720595.1		n.176-14681_176-14680insATA	intron	N/A
ENSG00000294020	ENST00000720596.1		n.224-14681_224-14680insATA	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15185

AN:

144814

Hom.:

967

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0360

Gnomad AMI

AF:

0.0790

Gnomad AMR

AF:

0.0879

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.0789

Gnomad SAS

AF:

0.0922

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.145

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.0974

GnomAD2 exomes

AF:

0.0789

AC:

5921

AN:

75038

AF XY:

0.0815

show subpopulations

Gnomad AFR exome

AF:

0.00746

Gnomad AMR exome

AF:

0.0217

Gnomad ASJ exome

AF:

0.0837

Gnomad EAS exome

AF:

0.0182

Gnomad FIN exome

AF:

0.117

Gnomad NFE exome

AF:

0.0837

Gnomad OTH exome

AF:

0.0782

GnomAD4 exome

AF:

0.0885

AC:

57141

AN:

645770

Hom.:

1606

Cov.:

AF XY:

0.0908

AC XY:

30371

AN XY:

334318

show subpopulations

African (AFR)

AF:

0.0261

AC:

330

AN:

12648

American (AMR)

AF:

0.0402

AC:

580

AN:

14430

Ashkenazi Jewish (ASJ)

AF:

0.0743

AC:

1170

AN:

15752

East Asian (EAS)

AF:

0.0628

AC:

1385

AN:

22044

South Asian (SAS)

AF:

0.0614

AC:

2226

AN:

36258

European-Finnish (FIN)

AF:

0.101

AC:

2842

AN:

28068

Middle Eastern (MID)

AF:

0.0968

AC:

209

AN:

2158

European-Non Finnish (NFE)

AF:

0.0947

AC:

45991

AN:

485520

Other (OTH)

AF:

0.0833

AC:

2408

AN:

28892

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

2159

4319

6478

8638

10797

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1302

2604

3906

5208

6510

<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:

0.105

AC:

15170

AN:

144826

Hom.:

966

Cov.:

AF XY:

0.103

AC XY:

7227

AN XY:

70236

show subpopulations

African (AFR)

AF:

0.0360

AC:

1428

AN:

39678

American (AMR)

AF:

0.0879

AC:

1258

AN:

14310

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

352

AN:

3414

East Asian (EAS)

AF:

0.0788

AC:

391

AN:

4960

South Asian (SAS)

AF:

0.0918

AC:

418

AN:

4552

European-Finnish (FIN)

AF:

0.155

AC:

1337

AN:

8604

Middle Eastern (MID)

AF:

0.137

AC:

AN:

278

European-Non Finnish (NFE)

AF:

0.146

AC:

9688

AN:

66172

Other (OTH)

AF:

0.0963

AC:

190

AN:

1972

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

601

1203

1804

2406

3007

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<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:

0.102

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

0.12

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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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