Variant rs2241883 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000295834.8(FABP1):c.280A>G(p.Thr94Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,609,742 control chromosomes in the GnomAD database, including 78,312 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.29 ( 6995 hom., cov: 32)

Exomes 𝑓: 0.31 ( 71317 hom. )

Consequence

FABP1
ENST00000295834.8 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.553

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0013678968).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP1	NM_001443.3 linkuse as main transcript	c.280A>G	p.Thr94Ala	missense_variant	3/4	ENST00000295834.8	NP_001434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
FABP1	ENST00000295834.8 linkuse as main transcript	c.280A>G	p.Thr94Ala	missense_variant	3/4	1	NM_001443.3	ENSP00000295834	P1
FABP1	ENST00000393750.3 linkuse as main transcript	c.280A>G	p.Thr94Ala	missense_variant	3/3	2		ENSP00000377351
FABP1	ENST00000495375.1 linkuse as main transcript	n.566A>G		non_coding_transcript_exon_variant	4/4	3

Frequencies

GnomAD3 genomes

AF:

0.287

AC:

43552

AN:

151928

Hom.:

6991

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.409

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.340

Gnomad EAS

AF:

0.216

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.503

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.289

GnomAD3 exomes

AF:

0.303

AC:

75214

AN:

248312

Hom.:

12506

AF XY:

0.299

AC XY:

40183

AN XY:

134296

show subpopulations

Gnomad AFR exome

AF:

0.166

Gnomad AMR exome

AF:

0.308

Gnomad ASJ exome

AF:

0.335

Gnomad EAS exome

AF:

0.204

Gnomad SAS exome

AF:

0.174

Gnomad FIN exome

AF:

0.492

Gnomad NFE exome

AF:

0.332

Gnomad OTH exome

AF:

0.305

GnomAD4 exome

AF:

0.307

AC:

446857

AN:

1457694

Hom.:

71317

Cov.:

AF XY:

0.304

AC XY:

220408

AN XY:

725192

show subpopulations

Gnomad4 AFR exome

AF:

0.165

Gnomad4 AMR exome

AF:

0.308

Gnomad4 ASJ exome

AF:

0.340

Gnomad4 EAS exome

AF:

0.222

Gnomad4 SAS exome

AF:

0.174

Gnomad4 FIN exome

AF:

0.481

Gnomad4 NFE exome

AF:

0.316

Gnomad4 OTH exome

AF:

0.298

GnomAD4 genome

AF:

0.287

AC:

43584

AN:

152048

Hom.:

6995

Cov.:

AF XY:

0.290

AC XY:

21575

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.172

Gnomad4 AMR

AF:

0.298

Gnomad4 ASJ

AF:

0.340

Gnomad4 EAS

AF:

0.216

Gnomad4 SAS

AF:

0.158

Gnomad4 FIN

AF:

0.503

Gnomad4 NFE

AF:

0.331

Gnomad4 OTH

AF:

0.287

Alfa

AF:

0.314

Hom.:

19433

Bravo

AF:

0.272

TwinsUK

AF:

0.312

AC:

1157

ALSPAC

AF:

0.314

AC:

1211

ESP6500AA

AF:

0.167

AC:

736

ESP6500EA

AF:

0.323

AC:

2774

ExAC

AF:

0.298

AC:

36216

Asia WGS

AF:

0.227

AC:

787

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

DANN

Benign

0.86

DEOGEN2

Benign

0.055

T;.

Eigen

Benign

-0.60

Eigen_PC

Benign

-0.54

FATHMM_MKL

Benign

0.19

LIST_S2

Benign

0.36

T;T

MetaRNN

Benign

0.0014

T;T

MetaSVM

Benign

-0.93

MutationAssessor

Uncertain

2.1

M;.

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.29

PROVEAN

Benign

-1.9

N;N

REVEL

Benign

0.066

Sift

Benign

0.56

T;T

Sift4G

Benign

0.69

T;T

Polyphen

0.0

B;B

Vest4

0.098

MPC

0.25

ClinPred

0.0055

GERP RS

1.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.23

gMVP

0.48

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over