Variant rs4301822 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001638.4(APOF):c.932T>C(p.Ile311Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0308 in 1,613,896 control chromosomes in the GnomAD database, including 12,488 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 6566 hom., cov: 32)

Exomes 𝑓: 0.017 ( 5922 hom. )

Consequence

APOF
NM_001638.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0160

Variant links:

Genes affected

APOF (HGNC:615): (apolipoprotein F) The product of this gene is one of the minor apolipoproteins found in plasma. This protein forms complexes with lipoproteins and may be involved in transport and/or esterification of cholesterol. [provided by RefSeq, Jul 2008]

APOF 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=4.9995535E-5).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOF	NM_001638.4 link	c.932T>C	p.Ile311Thr	missense_variant	2/2	ENST00000398189.4	NP_001629.1	Q13790

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOF	ENST00000398189.4 link	c.932T>C	p.Ile311Thr	missense_variant	2/2	1	NM_001638.4	ENSP00000381250.3		Q13790

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24436

AN:

152090

Hom.:

6532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.554

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0673

Gnomad ASJ

AF:

0.0237

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00249

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00237

Gnomad OTH

AF:

0.107

GnomAD3 exomes

AF:

0.0421

AC:

10487

AN:

249188

Hom.:

2586

AF XY:

0.0325

AC XY:

4388

AN XY:

135196

show subpopulations

Gnomad AFR exome

AF:

0.572

Gnomad AMR exome

AF:

0.0290

Gnomad ASJ exome

AF:

0.0229

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00118

Gnomad FIN exome

AF:

0.0000464

Gnomad NFE exome

AF:

0.00214

Gnomad OTH exome

AF:

0.0217

GnomAD4 exome

AF:

0.0173

AC:

25226

AN:

1461688

Hom.:

5922

Cov.:

AF XY:

0.0149

AC XY:

10842

AN XY:

727122

show subpopulations

Gnomad4 AFR exome

AF:

0.575

Gnomad4 AMR exome

AF:

0.0337

Gnomad4 ASJ exome

AF:

0.0215

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00114

Gnomad4 FIN exome

AF:

0.0000562

Gnomad4 NFE exome

AF:

0.00123

Gnomad4 OTH exome

AF:

0.0378

GnomAD4 genome

AF:

0.161

AC:

24524

AN:

152208

Hom.:

6566

Cov.:

AF XY:

0.156

AC XY:

11600

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.555

Gnomad4 AMR

AF:

0.0673

Gnomad4 ASJ

AF:

0.0237

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00237

Gnomad4 OTH

AF:

0.106

Alfa

AF:

0.0337

Hom.:

2400

Bravo

AF:

0.184

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00130

AC:

ESP6500AA

AF:

0.540

AC:

2014

ESP6500EA

AF:

0.00453

AC:

ExAC

AF:

0.0504

AC:

6090

Asia WGS

AF:

0.0310

AC:

110

AN:

3478

EpiCase

AF:

0.00300

EpiControl

AF:

0.00379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.57

CADD

Benign

8.1

DANN

Benign

0.85

DEOGEN2

Benign

0.045

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.0064

LIST_S2

Benign

0.46

MetaRNN

Benign

0.000050

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.69

PrimateAI

Benign

0.32

PROVEAN

Benign

-1.0

REVEL

Benign

0.020

Sift

Benign

0.068

Sift4G

Uncertain

0.026

Polyphen

0.014

Vest4

0.033

MPC

0.14

ClinPred

0.0084

GERP RS

-0.83

Varity_R

0.059

gMVP

0.12

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