rs619054

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

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

The NM_001371904.1(APOA5):c.*31C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,604,378 control chromosomes in the GnomAD database, including 42,295 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 3246 hom., cov: 33)

Exomes 𝑓: 0.23 ( 39049 hom. )

Consequence

APOA5
NM_001371904.1 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.411

Publications

39 publications found

Variant links:

Genes affected

APOA5 (HGNC:17288): (apolipoprotein A5) The protein encoded by this gene is an apolipoprotein that plays an important role in regulating the plasma triglyceride levels, a major risk factor for coronary artery disease. It is a component of high density lipoprotein and is highly similar to a rat protein that is upregulated in response to liver injury. Mutations in this gene have been associated with hypertriglyceridemia and hyperlipoproteinemia type 5. This gene is located proximal to the apolipoprotein gene cluster on chromosome 11q23. Alternatively spliced transcript variants encoding the same protein have been identified. [provided by RefSeq, Oct 2009]

APOA5 Gene-Disease associations (from GenCC):

hypertriglyceridemia 1
Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
hyperlipoproteinemia type V
Inheritance: AD, SD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp

APOA5 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 (BayesDel_noAF=-0.78).

BP6

Variant 11-116790097-G-A is Benign according to our data. Variant chr11-116790097-G-A is described in ClinVar as Benign. ClinVar VariationId is 1293389.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
APOA5	NM_001371904.1 link	c.*31C>T	3_prime_UTR_variant	Exon 3 of 3	ENST00000227665.9	NP_001358833.1
APOA5	NM_001166598.2 link	c.*31C>T	3_prime_UTR_variant	Exon 4 of 4		NP_001160070.1
APOA5	NM_052968.5 link	c.*31C>T	3_prime_UTR_variant	Exon 4 of 4		NP_443200.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
APOA5	ENST00000227665.9 link	c.*31C>T	3_prime_UTR_variant	Exon 3 of 3	1	NM_001371904.1	ENSP00000227665.4
APOA5	ENST00000433069.2 link	c.*31C>T	3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000399701.2
APOA5	ENST00000673688.1 link	c.*31C>T	3_prime_UTR_variant	Exon 3 of 3			ENSP00000501141.1
APOA5	ENST00000542499.5 link	c.*31C>T	3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000445002.1

Frequencies

GnomAD3 genomes

AF:

0.192

AC:

29131

AN:

152104

Hom.:

3240

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.00366

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.204

GnomAD2 exomes

AF:

0.189

AC:

45691

AN:

241740

AF XY:

0.194

show subpopulations

Gnomad AFR exome

AF:

0.116

Gnomad AMR exome

AF:

0.129

Gnomad ASJ exome

AF:

0.260

Gnomad EAS exome

AF:

0.00151

Gnomad FIN exome

AF:

0.219

Gnomad NFE exome

AF:

0.247

Gnomad OTH exome

AF:

0.219

GnomAD4 exome

AF:

0.225

AC:

327237

AN:

1452156

Hom.:

39049

Cov.:

AF XY:

0.225

AC XY:

162544

AN XY:

722306

show subpopulations

African (AFR)

AF:

0.114

AC:

3802

AN:

33280

American (AMR)

AF:

0.134

AC:

5908

AN:

44000

Ashkenazi Jewish (ASJ)

AF:

0.258

AC:

6698

AN:

25982

East Asian (EAS)

AF:

0.000939

AC:

AN:

39422

South Asian (SAS)

AF:

0.146

AC:

12430

AN:

85376

European-Finnish (FIN)

AF:

0.223

AC:

11834

AN:

53106

Middle Eastern (MID)

AF:

0.247

AC:

1422

AN:

5746

European-Non Finnish (NFE)

AF:

0.246

AC:

272118

AN:

1105254

Other (OTH)

AF:

0.217

AC:

12988

AN:

59990

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

14266

28532

42799

57065

71331

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8932

17864

26796

35728

44660

<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:

0.192

AC:

29162

AN:

152222

Hom.:

3246

Cov.:

AF XY:

0.189

AC XY:

14035

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.118

AC:

4883

AN:

41550

American (AMR)

AF:

0.171

AC:

2623

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.252

AC:

875

AN:

3470

East Asian (EAS)

AF:

0.00367

AC:

AN:

5182

South Asian (SAS)

AF:

0.131

AC:

632

AN:

4832

European-Finnish (FIN)

AF:

0.222

AC:

2351

AN:

10586

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.251

AC:

17042

AN:

67990

Other (OTH)

AF:

0.202

AC:

427

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1185

2370

3554

4739

5924

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.234

Hom.:

6228

Bravo

AF:

0.182

Asia WGS

AF:

0.0720

AC:

250

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Sep 17, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.7

(source)

DANN

Benign

0.75

PhyloP100

-0.41

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over