Genetic Variant FABP1:c.333+197T>C (chr2-88124297-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001443.3(FABP1):c.333+197T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 518,684 control chromosomes in the GnomAD database, including 16,974 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 0.19 ( 3532 hom., cov: 32)

Exomes 𝑓: 0.25 ( 13442 hom. )

Consequence

FABP1
NM_001443.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240

Publications

20 publications found

Variant links:

Genes affected

FABP1 (HGNC:3555): (fatty acid binding protein 1) This gene encodes the fatty acid binding protein found in liver. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. This protein and FABP6 (the ileal fatty acid binding protein) are also able to bind bile acids. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. [provided by RefSeq, Mar 2011]

FABP1 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).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP1	NM_001443.3 link	c.333+197T>C		intron_variant	Intron 3 of 3	ENST00000295834.8	NP_001434.1	P07148Q6FGL7Q05CP7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FABP1	ENST00000295834.8 link	c.333+197T>C	intron_variant	Intron 3 of 3	1	NM_001443.3	ENSP00000295834.3	P07148
FABP1	ENST00000495375.1 link	n.816T>C	non_coding_transcript_exon_variant	Exon 4 of 4	3
FABP1	ENST00000393750.3 link	c.*155T>C	3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000377351.3	A8MW49

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

28989

AN:

151984

Hom.:

3529

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.533

Gnomad SAS

AF:

0.492

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.258

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.193

GnomAD4 exome

AF:

0.248

AC:

90900

AN:

366582

Hom.:

13442

Cov.:

AF XY:

0.257

AC XY:

49117

AN XY:

190820

show subpopulations

African (AFR)

AF:

0.0949

AC:

803

AN:

8460

American (AMR)

AF:

0.147

AC:

1341

AN:

9140

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

2476

AN:

11914

East Asian (EAS)

AF:

0.505

AC:

12140

AN:

24034

South Asian (SAS)

AF:

0.466

AC:

13406

AN:

28754

European-Finnish (FIN)

AF:

0.134

AC:

4018

AN:

29980

Middle Eastern (MID)

AF:

0.241

AC:

423

AN:

1754

European-Non Finnish (NFE)

AF:

0.222

AC:

51175

AN:

230070

Other (OTH)

AF:

0.228

AC:

5118

AN:

22476

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

3019

6038

9057

12076

15095

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

242

484

726

968

1210

<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:

0.191

AC:

28992

AN:

152102

Hom.:

3532

Cov.:

AF XY:

0.194

AC XY:

14464

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.103

AC:

4259

AN:

41514

American (AMR)

AF:

0.148

AC:

2258

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

736

AN:

3470

East Asian (EAS)

AF:

0.533

AC:

2732

AN:

5130

South Asian (SAS)

AF:

0.492

AC:

2372

AN:

4822

European-Finnish (FIN)

AF:

0.110

AC:

1167

AN:

10608

Middle Eastern (MID)

AF:

0.267

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.218

AC:

14826

AN:

67962

Other (OTH)

AF:

0.200

AC:

421

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1186

2372

3559

4745

5931

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

338

676

1014

1352

1690

<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:

0.215

Hom.:

12265

Bravo

AF:

0.184

Asia WGS

AF:

0.461

AC:

1601

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

7.7

(source)

DANN

Benign

0.52

PhyloP100

0.24

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

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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