Variant 8-81480601-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001442.3(FABP4):c.74-3T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 1,603,318 control chromosomes in the GnomAD database, including 194 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.010 ( 17 hom., cov: 32)

Exomes 𝑓: 0.015 ( 177 hom. )

Consequence

FABP4
NM_001442.3 splice_region, intron

Scores

Splicing: ADA: 0.00003577

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0170

Variant links:

Genes affected

FABP4 (HGNC:3559): (fatty acid binding protein 4) FABP4 encodes the fatty acid binding protein found in adipocytes. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. [provided by RefSeq, Jul 2008]

FABP4 links:

FABP4 (HGNC:):

FABP4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 8-81480601-A-G is Benign according to our data. Variant chr8-81480601-A-G is described in ClinVar as [Benign]. Clinvar id is 769744.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0145 (21082/1451022) while in subpopulation NFE AF= 0.0169 (18674/1107292). AF 95% confidence interval is 0.0167. There are 177 homozygotes in gnomad4_exome. There are 10305 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 17 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP4	NM_001442.3 linkuse as main transcript	c.74-3T>C		splice_region_variant, intron_variant		ENST00000256104.5	NP_001433.1	P15090E7DVW4
LOC101927118	XR_001745980.2 linkuse as main transcript	n.517+18627A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
FABP4	ENST00000256104.5 linkuse as main transcript	c.74-3T>C	splice_region_variant, intron_variant	1	NM_001442.3	ENSP00000256104.4	P15090
FABP4	ENST00000518669.5 linkuse as main transcript	n.143-137T>C	intron_variant	3
FABP4	ENST00000522659.1 linkuse as main transcript	n.70-3T>C	splice_region_variant, intron_variant	3		ENSP00000428385.1	E5RIR0
ENSG00000253859	ENST00000524085.2 linkuse as main transcript	n.299-17316A>G	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0104

AC:

1590

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00290

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00831

Gnomad ASJ

AF:

0.0112

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.0235

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0150

Gnomad OTH

AF:

0.0110

GnomAD3 exomes

AF:

0.0102

AC:

2468

AN:

241506

Hom.:

AF XY:

0.0102

AC XY:

1326

AN XY:

130596

show subpopulations

Gnomad AFR exome

AF:

0.00256

Gnomad AMR exome

AF:

0.00480

Gnomad ASJ exome

AF:

0.0102

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00189

Gnomad FIN exome

AF:

0.0229

Gnomad NFE exome

AF:

0.0143

Gnomad OTH exome

AF:

0.00978

GnomAD4 exome

AF:

0.0145

AC:

21082

AN:

1451022

Hom.:

177

Cov.:

AF XY:

0.0143

AC XY:

10305

AN XY:

721274

show subpopulations

Gnomad4 AFR exome

AF:

0.00189

Gnomad4 AMR exome

AF:

0.00472

Gnomad4 ASJ exome

AF:

0.00948

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00180

Gnomad4 FIN exome

AF:

0.0191

Gnomad4 NFE exome

AF:

0.0169

Gnomad4 OTH exome

AF:

0.0120

GnomAD4 genome

AF:

0.0104

AC:

1590

AN:

152296

Hom.:

Cov.:

AF XY:

0.0106

AC XY:

792

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00289

Gnomad4 AMR

AF:

0.00830

Gnomad4 ASJ

AF:

0.0112

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0235

Gnomad4 NFE

AF:

0.0150

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.0129

Hom.:

Bravo

AF:

0.00944

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.0126

EpiControl

AF:

0.0148

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

Labcorp Genetics (formerly Invitae), Labcorp

Jul 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

8.9

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000036

dbscSNV1_RF

Benign

0.0

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