chr2-21026844-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_000384.3(APOB):c.2188G>A(p.Val730Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 1,613,814 control chromosomes in the GnomAD database, including 980 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.027 ( 55 hom., cov: 32)

Exomes 𝑓: 0.033 ( 925 hom. )

Consequence

APOB
NM_000384.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:3B:17

Conservation

PhyloP100: 1.04

Publications

34 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005947888).

BP6

Variant 2-21026844-C-T is Benign according to our data. Variant chr2-21026844-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 128421.

BS1

Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0267 (4071/152286) while in subpopulation AMR AF = 0.0354 (542/15296). AF 95% confidence interval is 0.0342. There are 55 homozygotes in GnomAd4. There are 2013 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 55 AD,AR,SD gene

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOB	NM_000384.3	MANE Select	c.2188G>A	p.Val730Ile	missense	Exon 15 of 29	NP_000375.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
APOB	ENST00000233242.5	TSL:1 MANE Select	c.2188G>A	p.Val730Ile	missense	Exon 15 of 29	ENSP00000233242.1
APOB	ENST00000399256.4	TSL:1	c.2188G>A	p.Val730Ile	missense	Exon 15 of 17	ENSP00000382200.4
APOB	ENST00000673739.2		n.*1494G>A		non_coding_transcript_exon	Exon 14 of 25	ENSP00000501110.2

Frequencies

GnomAD3 genomes

AF:

0.0268

AC:

4072

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00656

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0355

Gnomad ASJ

AF:

0.0568

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00311

Gnomad FIN

AF:

0.0520

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0354

Gnomad OTH

AF:

0.0354

GnomAD2 exomes

AF:

0.0271

AC:

6818

AN:

251322

AF XY:

0.0268

show subpopulations

Gnomad AFR exome

AF:

0.00591

Gnomad AMR exome

AF:

0.0235

Gnomad ASJ exome

AF:

0.0511

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0480

Gnomad NFE exome

AF:

0.0355

Gnomad OTH exome

AF:

0.0326

GnomAD4 exome

AF:

0.0335

AC:

48895

AN:

1461528

Hom.:

925

Cov.:

AF XY:

0.0326

AC XY:

23676

AN XY:

727086

show subpopulations

African (AFR)

AF:

0.00508

AC:

170

AN:

33478

American (AMR)

AF:

0.0247

AC:

1106

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0489

AC:

1279

AN:

26132

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39692

South Asian (SAS)

AF:

0.00398

AC:

343

AN:

86254

European-Finnish (FIN)

AF:

0.0450

AC:

2401

AN:

53414

Middle Eastern (MID)

AF:

0.00971

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0375

AC:

41666

AN:

1111682

Other (OTH)

AF:

0.0310

AC:

1873

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

2260

4520

6781

9041

11301

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1578

3156

4734

6312

7890

<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:

0.0267

AC:

4071

AN:

152286

Hom.:

Cov.:

AF XY:

0.0270

AC XY:

2013

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.00654

AC:

272

AN:

41568

American (AMR)

AF:

0.0354

AC:

542

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0568

AC:

197

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5184

South Asian (SAS)

AF:

0.00311

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0520

AC:

551

AN:

10596

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0354

AC:

2408

AN:

68032

Other (OTH)

AF:

0.0350

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

201

403

604

806

1007

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<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:

0.0318

Hom.:

110

Bravo

AF:

0.0251

TwinsUK

AF:

0.0402

AC:

149

ALSPAC

AF:

0.0420

AC:

162

ESP6500AA

AF:

0.00658

AC:

ESP6500EA

AF:

0.0351

AC:

302

ExAC

AF:

0.0250

AC:

3035

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.0348

EpiControl

AF:

0.0375

ClinVar

ClinVar submissions as Germline

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (6)

Familial hypercholesterolemia (4)

Hypercholesterolemia, familial, 1 (3)

Hypercholesterolemia, autosomal dominant, type B (2)

not provided (2)

Cardiovascular phenotype (1)

Familial hypobetalipoproteinemia 1 (1)

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

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.071

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.014

Eigen

Benign

0.15

Eigen_PC

Benign

0.17

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.63

MetaRNN

Benign

0.0059

MetaSVM

Benign

-1.1

PhyloP100

1.0

PrimateAI

Benign

0.39

PROVEAN

Benign

-0.42

REVEL

Benign

0.13

Sift

Benign

0.16

Sift4G

Pathogenic

0.0

Vest4

0.15

MPC

0.042

ClinPred

0.011

GERP RS

3.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

gMVP

0.76

Mutation Taster

=96/4

disease causing (ClinVar)

(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

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over