Variant 4-119319083-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_000134.4(FABP2):c.357A>G(p.Val119=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 1,590,014 control chromosomes in the GnomAD database, including 86,219 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 8810 hom., cov: 32)

Exomes 𝑓: 0.32 ( 77409 hom. )

Consequence

FABP2
NM_000134.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.09

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 4-119319083-T-C is Benign according to our data. Variant chr4-119319083-T-C is described in ClinVar as [Benign]. Clinvar id is 1259953.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FABP2	NM_000134.4 linkuse as main transcript	c.357A>G	p.Val119=	synonymous_variant	4/4	ENST00000274024.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP2	ENST00000274024.4 linkuse as main transcript	c.357A>G	p.Val119=	synonymous_variant	4/4	1	NM_000134.4	P1

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51157

AN:

151648

Hom.:

8793

Cov.:

show subpopulations

Gnomad AFR

AF:

0.385

Gnomad AMI

AF:

0.343

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.387

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.341

GnomAD3 exomes

AF:

0.309

AC:

73543

AN:

237654

Hom.:

11932

AF XY:

0.302

AC XY:

39026

AN XY:

129196

show subpopulations

Gnomad AFR exome

AF:

0.382

Gnomad AMR exome

AF:

0.307

Gnomad ASJ exome

AF:

0.212

Gnomad EAS exome

AF:

0.395

Gnomad SAS exome

AF:

0.207

Gnomad FIN exome

AF:

0.303

Gnomad NFE exome

AF:

0.324

Gnomad OTH exome

AF:

0.292

GnomAD4 exome

AF:

0.324

AC:

465417

AN:

1438248

Hom.:

77409

Cov.:

AF XY:

0.319

AC XY:

228406

AN XY:

716138

show subpopulations

Gnomad4 AFR exome

AF:

0.378

Gnomad4 AMR exome

AF:

0.310

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.356

Gnomad4 SAS exome

AF:

0.206

Gnomad4 FIN exome

AF:

0.298

Gnomad4 NFE exome

AF:

0.335

Gnomad4 OTH exome

AF:

0.314

GnomAD4 genome

AF:

0.337

AC:

51219

AN:

151766

Hom.:

8810

Cov.:

AF XY:

0.335

AC XY:

24814

AN XY:

74166

show subpopulations

Gnomad4 AFR

AF:

0.385

Gnomad4 AMR

AF:

0.309

Gnomad4 ASJ

AF:

0.205

Gnomad4 EAS

AF:

0.388

Gnomad4 SAS

AF:

0.209

Gnomad4 FIN

AF:

0.295

Gnomad4 NFE

AF:

0.333

Gnomad4 OTH

AF:

0.342

Alfa

AF:

0.329

Hom.:

10526

Bravo

AF:

0.348

Asia WGS

AF:

0.294

AC:

1020

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.083

DANN

Benign

0.44

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over