Genetic Variant FABP3:c.246+79G>A (chr1-31369306-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_004102.5(FABP3):c.246+79G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 1,478,564 control chromosomes in the GnomAD database, including 980 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.030 ( 79 hom., cov: 32)

Exomes 𝑓: 0.035 ( 901 hom. )

Consequence

FABP3
NM_004102.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.293

Publications

10 publications found

Variant links:

Genes affected

FABP3 (HGNC:3557): (fatty acid binding protein 3) The intracellular fatty acid-binding proteins (FABPs) belongs to a multigene family. FABPs are divided into at least three distinct types, namely the hepatic-, intestinal- and cardiac-type. They form 14-15 kDa proteins and are thought to participate in the uptake, intracellular metabolism and/or transport of long-chain fatty acids. They may also be responsible in the modulation of cell growth and proliferation. Fatty acid-binding protein 3 gene contains four exons and its function is to arrest growth of mammary epithelial cells. This gene is a candidate tumor suppressor gene for human breast cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

FABP3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0298 (4544/152242) while in subpopulation NFE AF = 0.0382 (2598/68000). AF 95% confidence interval is 0.037. There are 79 homozygotes in GnomAd4. There are 2113 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 79 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
FABP3	NM_004102.5 link	c.246+79G>A	intron_variant	Intron 2 of 3	ENST00000373713.7	NP_004093.1	P05413A0A384MDY5
FABP3	NM_001320996.2 link	c.279+79G>A	intron_variant	Intron 2 of 3		NP_001307925.1
FABP3	XM_011541007.4 link	c.246+79G>A	intron_variant	Intron 2 of 3		XP_011539309.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FABP3	ENST00000373713.7 link	c.246+79G>A	intron_variant	Intron 2 of 3	1	NM_004102.5	ENSP00000362817.2	P05413
FABP3	ENST00000482018.1 link	c.246+79G>A	intron_variant	Intron 4 of 5	5		ENSP00000473982.1	S4R371
FABP3	ENST00000497275.5 link	n.206+79G>A	intron_variant	Intron 1 of 2	2
FABP3	ENST00000498148.5 link	n.246+79G>A	intron_variant	Intron 2 of 4	2		ENSP00000474078.1	S4R3A2

Frequencies

GnomAD3 genomes

AF:

0.0299

AC:

4543

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0167

Gnomad AMI

AF:

0.0264

Gnomad AMR

AF:

0.0274

Gnomad ASJ

AF:

0.0775

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0106

Gnomad FIN

AF:

0.0374

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0382

Gnomad OTH

AF:

0.0363

GnomAD4 exome

AF:

0.0347

AC:

45974

AN:

1326322

Hom.:

901

Cov.:

AF XY:

0.0344

AC XY:

22624

AN XY:

656868

show subpopulations

African (AFR)

AF:

0.0163

AC:

501

AN:

30682

American (AMR)

AF:

0.0187

AC:

746

AN:

39848

Ashkenazi Jewish (ASJ)

AF:

0.0758

AC:

1654

AN:

21824

East Asian (EAS)

AF:

0.0000258

AC:

AN:

38824

South Asian (SAS)

AF:

0.0115

AC:

858

AN:

74556

European-Finnish (FIN)

AF:

0.0401

AC:

2053

AN:

51170

Middle Eastern (MID)

AF:

0.0495

AC:

262

AN:

5298

European-Non Finnish (NFE)

AF:

0.0376

AC:

37948

AN:

1008628

Other (OTH)

AF:

0.0352

AC:

1951

AN:

55492

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

2149

4298

6447

8596

10745

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1408

2816

4224

5632

7040

<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:

0.0298

AC:

4544

AN:

152242

Hom.:

Cov.:

AF XY:

0.0284

AC XY:

2113

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.0167

AC:

693

AN:

41542

American (AMR)

AF:

0.0273

AC:

418

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0775

AC:

269

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5194

South Asian (SAS)

AF:

0.0108

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.0374

AC:

397

AN:

10614

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0382

AC:

2598

AN:

68000

Other (OTH)

AF:

0.0359

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

234

468

701

935

1169

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0362

Hom.:

179

Bravo

AF:

0.0289

Asia WGS

AF:

0.00520

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.1

(source)

DANN

Benign

0.17

PhyloP100

-0.29

Mutation Taster

=100/0

polymorphism

(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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over