Genetic Variant APOD:c.*110G>A (chr3-195568790-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001647.4(APOD):c.*110G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 762,516 control chromosomes in the GnomAD database, including 164,886 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 0.56 ( 25897 hom., cov: 26)

Exomes 𝑓: 0.66 ( 138989 hom. )

Consequence

APOD
NM_001647.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Publications

11 publications found

Variant links:

Genes affected

APOD (HGNC:612): (apolipoprotein D) This gene encodes a component of high density lipoprotein that has no marked similarity to other apolipoprotein sequences. It has a high degree of homology to plasma retinol-binding protein and other members of the alpha 2 microglobulin protein superfamily of carrier proteins, also known as lipocalins. This glycoprotein is closely associated with the enzyme lecithin:cholesterol acyltransferase - an enzyme involved in lipoprotein metabolism. [provided by RefSeq, Aug 2008]

APOD links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001647.4. 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
	APOD	NM_001647.4	MANE Select	c.*110G>A		3_prime_UTR	Exon 5 of 5	NP_001638.1	P05090

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
APOD	ENST00000343267.8	TSL:1 MANE Select	c.*110G>A	3_prime_UTR	Exon 5 of 5	ENSP00000345179.3	P05090
APOD	ENST00000953531.1		c.*110G>A	3_prime_UTR	Exon 6 of 6	ENSP00000623590.1
APOD	ENST00000852526.1		c.*110G>A	3_prime_UTR	Exon 6 of 6	ENSP00000522585.1

Frequencies

GnomAD3 genomes

AF:

0.565

AC:

81170

AN:

143750

Hom.:

25884

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.787

Gnomad AMR

AF:

0.713

Gnomad ASJ

AF:

0.714

Gnomad EAS

AF:

0.522

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.749

Gnomad MID

AF:

0.571

Gnomad NFE

AF:

0.686

Gnomad OTH

AF:

0.610

GnomAD4 exome

AF:

0.658

AC:

406979

AN:

618704

Hom.:

138989

Cov.:

AF XY:

0.650

AC XY:

213187

AN XY:

327814

show subpopulations

African (AFR)

AF:

0.187

AC:

3032

AN:

16254

American (AMR)

AF:

0.786

AC:

28009

AN:

35620

Ashkenazi Jewish (ASJ)

AF:

0.721

AC:

12338

AN:

17122

East Asian (EAS)

AF:

0.532

AC:

18341

AN:

34450

South Asian (SAS)

AF:

0.487

AC:

28238

AN:

57966

European-Finnish (FIN)

AF:

0.725

AC:

34580

AN:

47676

Middle Eastern (MID)

AF:

0.552

AC:

1572

AN:

2848

European-Non Finnish (NFE)

AF:

0.696

AC:

260660

AN:

374754

Other (OTH)

AF:

0.631

AC:

20209

AN:

32014

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

Heterozygous variant carriers

6571

13142

19713

26284

32855

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2486

4972

7458

9944

12430

<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:

0.565

AC:

81194

AN:

143812

Hom.:

25897

Cov.:

AF XY:

0.566

AC XY:

39704

AN XY:

70156

show subpopulations

African (AFR)

AF:

0.214

AC:

7621

AN:

35590

American (AMR)

AF:

0.714

AC:

10378

AN:

14544

Ashkenazi Jewish (ASJ)

AF:

0.714

AC:

2469

AN:

3458

East Asian (EAS)

AF:

0.522

AC:

2529

AN:

4848

South Asian (SAS)

AF:

0.491

AC:

2274

AN:

4634

European-Finnish (FIN)

AF:

0.749

AC:

7488

AN:

9998

Middle Eastern (MID)

AF:

0.556

AC:

149

AN:

268

European-Non Finnish (NFE)

AF:

0.686

AC:

46360

AN:

67580

Other (OTH)

AF:

0.611

AC:

1215

AN:

1988

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

1276

2553

3829

5106

6382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

672

1344

2016

2688

3360

<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:

0.618

Hom.:

54537

Bravo

AF:

0.524

Asia WGS

AF:

0.514

AC:

1792

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.7

(source)

DANN

Benign

0.64

PhyloP100

-0.0070

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over