dbSNP rs40831: APOBR:p.Ala695Ala (chr16-28497126-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_018690.4(APOBR):c.2085A>G(p.Ala695Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 1,603,570 control chromosomes in the GnomAD database, including 158,570 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.46 ( 16698 hom., cov: 32)

Exomes 𝑓: 0.44 ( 141872 hom. )

Consequence

APOBR
NM_018690.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.756

Publications

35 publications found

Variant links:

Genes affected

APOBR (HGNC:24087): (apolipoprotein B receptor) Apolipoprotein B48 receptor is a macrophage receptor that binds to the apolipoprotein B48 of dietary triglyceride (TG)-rich lipoproteins. This receptor may provide essential lipids, lipid-soluble vitamins and other nutrients to reticuloendothelial cells. If overwhelmed with elevated plasma triglyceride, the apolipoprotein B48 receptor may contribute to foam cell formation, endothelial dysfunction, and atherothrombogenesis. [provided by RefSeq, Jul 2008]

APOBR 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 (BayesDel_noAF=-0.86).

BP7

Synonymous conserved (PhyloP=-0.756 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOBR	NM_018690.4 link	c.2085A>G	p.Ala695Ala	synonymous_variant	Exon 2 of 4	ENST00000564831.6	NP_061160.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOBR	ENST00000564831.6 link	c.2085A>G	p.Ala695Ala	synonymous_variant	Exon 2 of 4	1	NM_018690.4	ENSP00000457539.1

Frequencies

GnomAD3 genomes

AF:

0.463

AC:

70256

AN:

151894

Hom.:

16677

Cov.:

show subpopulations

Gnomad AFR

AF:

0.526

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.461

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.584

Gnomad FIN

AF:

0.512

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.430

Gnomad OTH

AF:

0.400

GnomAD2 exomes

AF:

0.457

AC:

105580

AN:

230918

AF XY:

0.457

show subpopulations

Gnomad AFR exome

AF:

0.528

Gnomad AMR exome

AF:

0.515

Gnomad ASJ exome

AF:

0.329

Gnomad EAS exome

AF:

0.338

Gnomad FIN exome

AF:

0.510

Gnomad NFE exome

AF:

0.423

Gnomad OTH exome

AF:

0.415

GnomAD4 exome

AF:

0.438

AC:

636192

AN:

1451558

Hom.:

141872

Cov.:

AF XY:

0.442

AC XY:

318382

AN XY:

721074

show subpopulations

African (AFR)

AF:

0.514

AC:

17156

AN:

33348

American (AMR)

AF:

0.523

AC:

22368

AN:

42784

Ashkenazi Jewish (ASJ)

AF:

0.324

AC:

8403

AN:

25904

East Asian (EAS)

AF:

0.304

AC:

11965

AN:

39372

South Asian (SAS)

AF:

0.569

AC:

48174

AN:

84602

European-Finnish (FIN)

AF:

0.507

AC:

26513

AN:

52318

Middle Eastern (MID)

AF:

0.264

AC:

1523

AN:

5760

European-Non Finnish (NFE)

AF:

0.429

AC:

474641

AN:

1107414

Other (OTH)

AF:

0.424

AC:

25449

AN:

60056

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

24421

48842

73262

97683

122104

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14566

29132

43698

58264

72830

<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:

0.463

AC:

70328

AN:

152012

Hom.:

16698

Cov.:

AF XY:

0.467

AC XY:

34717

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.526

AC:

21798

AN:

41462

American (AMR)

AF:

0.462

AC:

7067

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1103

AN:

3468

East Asian (EAS)

AF:

0.350

AC:

1798

AN:

5136

South Asian (SAS)

AF:

0.582

AC:

2805

AN:

4822

European-Finnish (FIN)

AF:

0.512

AC:

5416

AN:

10574

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.430

AC:

29208

AN:

67944

Other (OTH)

AF:

0.402

AC:

847

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1900

3799

5699

7598

9498

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

650

1300

1950

2600

3250

<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:

0.416

Hom.:

17180

Bravo

AF:

0.456

Asia WGS

AF:

0.508

AC:

1760

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.8

(source)

DANN

Benign

0.29

PhyloP100

-0.76

Mutation Taster

=100/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over