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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_000134.4(FABP2):c.241-10_241-5dupTATTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.036 ( 111 hom., cov: 0)

Exomes 𝑓: 0.022 ( 180 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:

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 -8 ACMG points.

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0364 (5270/144868) while in subpopulation SAS AF = 0.0472 (215/4556). AF 95% confidence interval is 0.042. There are 111 homozygotes in GnomAd4. There are 2514 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 111 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.241-10_241-5dupTATTAT		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_241-4insTATTAT	splice_region intron	N/A	ENSP00000274024.3	P12104
ENSG00000294020	ENST00000720595.1		n.176-14681_176-14680insATAATA	intron	N/A
ENSG00000294020	ENST00000720596.1		n.224-14681_224-14680insATAATA	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0364

AC:

5273

AN:

144856

Hom.:

111

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0426

Gnomad AMI

AF:

0.0158

Gnomad AMR

AF:

0.0336

Gnomad ASJ

AF:

0.0331

Gnomad EAS

AF:

0.0169

Gnomad SAS

AF:

0.0472

Gnomad FIN

AF:

0.0153

Gnomad MID

AF:

0.0789

Gnomad NFE

AF:

0.0368

Gnomad OTH

AF:

0.0454

GnomAD2 exomes

AF:

0.0212

AC:

1593

AN:

75038

AF XY:

0.0230

show subpopulations

Gnomad AFR exome

AF:

0.00947

Gnomad AMR exome

AF:

0.00586

Gnomad ASJ exome

AF:

0.0237

Gnomad EAS exome

AF:

0.00455

Gnomad FIN exome

AF:

0.0146

Gnomad NFE exome

AF:

0.0235

Gnomad OTH exome

AF:

0.0205

GnomAD4 exome

AF:

0.0224

AC:

14538

AN:

648600

Hom.:

180

Cov.:

AF XY:

0.0235

AC XY:

7901

AN XY:

335676

show subpopulations

African (AFR)

AF:

0.0304

AC:

385

AN:

12662

American (AMR)

AF:

0.0144

AC:

209

AN:

14466

Ashkenazi Jewish (ASJ)

AF:

0.0215

AC:

342

AN:

15894

East Asian (EAS)

AF:

0.0146

AC:

322

AN:

22116

South Asian (SAS)

AF:

0.0213

AC:

778

AN:

36444

European-Finnish (FIN)

AF:

0.0146

AC:

413

AN:

28196

Middle Eastern (MID)

AF:

0.0470

AC:

102

AN:

2168

European-Non Finnish (NFE)

AF:

0.0232

AC:

11313

AN:

487584

Other (OTH)

AF:

0.0232

AC:

674

AN:

29070

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.429

Heterozygous variant carriers

488

977

1465

1954

2442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

298

596

894

1192

1490

<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:

0.0364

AC:

5270

AN:

144868

Hom.:

111

Cov.:

AF XY:

0.0358

AC XY:

2514

AN XY:

70268

show subpopulations

African (AFR)

AF:

0.0425

AC:

1688

AN:

39674

American (AMR)

AF:

0.0335

AC:

479

AN:

14312

Ashkenazi Jewish (ASJ)

AF:

0.0331

AC:

113

AN:

3414

East Asian (EAS)

AF:

0.0169

AC:

AN:

4958

South Asian (SAS)

AF:

0.0472

AC:

215

AN:

4556

European-Finnish (FIN)

AF:

0.0153

AC:

132

AN:

8614

Middle Eastern (MID)

AF:

0.0755

AC:

AN:

278

European-Non Finnish (NFE)

AF:

0.0368

AC:

2435

AN:

66202

Other (OTH)

AF:

0.0451

AC:

AN:

1972

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

222

444

667

889

1111

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

192

256

320

<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:

0.0184

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 (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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4-119319647-CATAATAATAATAATA-CATAATAATAATAATAATAATA

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