NM_000384.3:c.12809G>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000384.3(APOB):c.12809G>C(p.Arg4270Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0302 in 1,613,894 control chromosomes in the GnomAD database, including 1,665 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.054 ( 394 hom., cov: 32)

Exomes 𝑓: 0.028 ( 1271 hom. )

Consequence

APOB
NM_000384.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:16

Conservation

PhyloP100: 0.137

Publications

39 publications found

Variant links:

Genes affected

APOB (HGNC:603): (apolipoprotein B) This gene product is the main apolipoprotein of chylomicrons and low density lipoproteins (LDL), and is the ligand for the LDL receptor. It occurs in plasma as two main isoforms, apoB-48 and apoB-100: the former is synthesized exclusively in the gut and the latter in the liver. The intestinal and the hepatic forms of apoB are encoded by a single gene from a single, very long mRNA. The two isoforms share a common N-terminal sequence. The shorter apoB-48 protein is produced after RNA editing of the apoB-100 transcript at residue 2180 (CAA->UAA), resulting in the creation of a stop codon, and early translation termination. Mutations in this gene or its regulatory region cause hypobetalipoproteinemia, normotriglyceridemic hypobetalipoproteinemia, and hypercholesterolemia due to ligand-defective apoB, diseases affecting plasma cholesterol and apoB levels. [provided by RefSeq, Dec 2019]

APOB Gene-Disease associations (from GenCC):

hypercholesterolemia, autosomal dominant, type B
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, G2P, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
familial hypobetalipoproteinemia 1
Inheritance: AR, AD, SD Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, ClinGen
homozygous familial hypercholesterolemia
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

APOB links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015838444).

BP6

Variant 2-21002613-C-G is Benign according to our data. Variant chr2-21002613-C-G is described in ClinVar as Benign. ClinVar VariationId is 255977.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000384.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOB	NM_000384.3	MANE Select	c.12809G>C	p.Arg4270Thr	missense	Exon 29 of 29	NP_000375.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOB	ENST00000233242.5	TSL:1 MANE Select	c.12809G>C	p.Arg4270Thr	missense	Exon 29 of 29	ENSP00000233242.1

Frequencies

GnomAD3 genomes

AF:

0.0538

AC:

8187

AN:

152068

Hom.:

388

Cov.:

show subpopulations

Gnomad AFR

AF:

0.104

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.0616

Gnomad EAS

AF:

0.0318

Gnomad SAS

AF:

0.0155

Gnomad FIN

AF:

0.0355

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0197

Gnomad OTH

AF:

0.0535

GnomAD2 exomes

AF:

0.0496

AC:

12448

AN:

251068

AF XY:

0.0414

show subpopulations

Gnomad AFR exome

AF:

0.108

Gnomad AMR exome

AF:

0.167

Gnomad ASJ exome

AF:

0.0611

Gnomad EAS exome

AF:

0.0291

Gnomad FIN exome

AF:

0.0371

Gnomad NFE exome

AF:

0.0204

Gnomad OTH exome

AF:

0.0417

GnomAD4 exome

AF:

0.0277

AC:

40532

AN:

1461708

Hom.:

1271

Cov.:

AF XY:

0.0264

AC XY:

19231

AN XY:

727156

show subpopulations

African (AFR)

AF:

0.108

AC:

3611

AN:

33460

American (AMR)

AF:

0.162

AC:

7224

AN:

44710

Ashkenazi Jewish (ASJ)

AF:

0.0620

AC:

1619

AN:

26124

East Asian (EAS)

AF:

0.0372

AC:

1478

AN:

39696

South Asian (SAS)

AF:

0.0133

AC:

1151

AN:

86252

European-Finnish (FIN)

AF:

0.0367

AC:

1962

AN:

53398

Middle Eastern (MID)

AF:

0.0165

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.0192

AC:

21314

AN:

1111920

Other (OTH)

AF:

0.0344

AC:

2078

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

2071

4142

6213

8284

10355

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

978

1956

2934

3912

4890

<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:

0.0540

AC:

8220

AN:

152186

Hom.:

394

Cov.:

AF XY:

0.0546

AC XY:

4060

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.104

AC:

4334

AN:

41514

American (AMR)

AF:

0.103

AC:

1569

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0616

AC:

214

AN:

3472

East Asian (EAS)

AF:

0.0319

AC:

165

AN:

5176

South Asian (SAS)

AF:

0.0156

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0355

AC:

376

AN:

10594

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0197

AC:

1337

AN:

68014

Other (OTH)

AF:

0.0549

AC:

116

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

361

722

1084

1445

1806

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0236

Hom.:

Bravo

AF:

0.0656

TwinsUK

AF:

0.0170

AC:

ALSPAC

AF:

0.0182

AC:

ESP6500AA

AF:

0.104

AC:

460

ESP6500EA

AF:

0.0209

AC:

180

ExAC

AF:

0.0456

AC:

5538

Asia WGS

AF:

0.0400

AC:

137

AN:

3478

EpiCase

AF:

0.0165

EpiControl

AF:

0.0167

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Hypercholesterolemia, familial, 1 (4)

not specified (4)

Familial hypercholesterolemia (2)

not provided (2)

Cardiovascular phenotype (1)

Familial hypobetalipoproteinemia 1 (1)

Hypercholesterolemia, autosomal dominant, type B (1)

Hypercholesterolemia, autosomal dominant, type B;C4551990:Familial hypobetalipoproteinemia 1 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

4.9

(source)

DANN

Benign

0.50

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.41

MetaRNN

Benign

0.0016

MetaSVM

Benign

-0.93

PhyloP100

0.14

PrimateAI

Benign

0.22

PROVEAN

Benign

-1.7

REVEL

Benign

0.017

Sift

Benign

0.10

Sift4G

Uncertain

0.049

Vest4

0.15

MPC

0.049

ClinPred

0.0039

GERP RS

-1.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

gMVP

0.46

Mutation Taster

=98/2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over