dbSNP rs3117581: APOM:c.270-138A>G (chr6-31657087-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_019101.3(APOM):c.270-138A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.085 in 756,386 control chromosomes in the GnomAD database, including 3,913 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 0.073 ( 524 hom., cov: 31)

Exomes 𝑓: 0.088 ( 3389 hom. )

Consequence

APOM
NM_019101.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0330

Publications

8 publications found

Variant links:

Genes affected

APOM (HGNC:13916): (apolipoprotein M) The protein encoded by this gene is an apolipoprotein and member of the lipocalin protein family. It is found associated with high density lipoproteins and to a lesser extent with low density lipoproteins and triglyceride-rich lipoproteins. The encoded protein is secreted through the plasma membrane but remains membrane-bound, where it is involved in lipid transport. Alternate splicing results in both coding and non-coding variants of this gene. [provided by RefSeq, Jan 2012]

APOM links:

Genome browser will be placed here

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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
APOM	NM_019101.3 link	c.270-138A>G	intron_variant	Intron 2 of 5	ENST00000375916.4	NP_061974.2
APOM	NM_001256169.2 link	c.54-138A>G	intron_variant	Intron 2 of 5		NP_001243098.1
APOM	NR_045828.2 link	n.311-138A>G	intron_variant	Intron 2 of 5
APOM	XM_006715150.4 link	c.174-138A>G	intron_variant	Intron 2 of 5		XP_006715213.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
APOM	ENST00000375916.4 link	c.270-138A>G	intron_variant	Intron 2 of 5	1	NM_019101.3	ENSP00000365081.3
APOM	ENST00000375920.8 link	c.54-138A>G	intron_variant	Intron 2 of 5	1		ENSP00000365085.4
APOM	ENST00000375918.6 link	c.54-138A>G	intron_variant	Intron 2 of 4	2		ENSP00000365083.2

Frequencies

GnomAD3 genomes

AF:

0.0726

AC:

11016

AN:

151778

Hom.:

524

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0484

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.0353

Gnomad ASJ

AF:

0.0398

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.00125

Gnomad FIN

AF:

0.0788

Gnomad MID

AF:

0.0223

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.0548

GnomAD4 exome

AF:

0.0881

AC:

53274

AN:

604492

Hom.:

3389

AF XY:

0.0842

AC XY:

26607

AN XY:

316008

show subpopulations

African (AFR)

AF:

0.0514

AC:

787

AN:

15312

American (AMR)

AF:

0.0260

AC:

616

AN:

23656

Ashkenazi Jewish (ASJ)

AF:

0.0418

AC:

670

AN:

16042

East Asian (EAS)

AF:

0.0000614

AC:

AN:

32598

South Asian (SAS)

AF:

0.00274

AC:

142

AN:

51876

European-Finnish (FIN)

AF:

0.0834

AC:

2666

AN:

31982

Middle Eastern (MID)

AF:

0.00756

AC:

AN:

2644

European-Non Finnish (NFE)

AF:

0.115

AC:

45828

AN:

399070

Other (OTH)

AF:

0.0812

AC:

2543

AN:

31312

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

2526

5052

7577

10103

12629

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

880

1760

2640

3520

4400

<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:

0.0725

AC:

11016

AN:

151894

Hom.:

524

Cov.:

AF XY:

0.0676

AC XY:

5021

AN XY:

74244

show subpopulations

African (AFR)

AF:

0.0484

AC:

2004

AN:

41428

American (AMR)

AF:

0.0352

AC:

538

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0398

AC:

138

AN:

3468

East Asian (EAS)

AF:

0.000194

AC:

AN:

5146

South Asian (SAS)

AF:

0.00125

AC:

AN:

4810

European-Finnish (FIN)

AF:

0.0788

AC:

832

AN:

10556

Middle Eastern (MID)

AF:

0.0240

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.108

AC:

7313

AN:

67900

Other (OTH)

AF:

0.0542

AC:

114

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

521

1042

1564

2085

2606

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0940

Hom.:

Bravo

AF:

0.0688

Asia WGS

AF:

0.00837

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.8

(source)

DANN

Benign

0.56

PhyloP100

-0.033

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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