Genetic Variant APOA5:c.162-43A>G (chr11-116791110-T-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001371904.1(APOA5):c.162-43A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 1,492,902 control chromosomes in the GnomAD database, including 640,542 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.93 ( 66650 hom., cov: 33)

Exomes 𝑓: 0.92 ( 573892 hom. )

Consequence

APOA5
NM_001371904.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.540

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 11-116791110-T-C is Benign according to our data. Variant chr11-116791110-T-C is described in ClinVar as [Benign]. Clinvar id is 1297445.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-116791110-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
APOA5	NM_001371904.1 link	c.162-43A>G	intron_variant	Intron 2 of 2	ENST00000227665.9	NP_001358833.1
APOA5	NM_001166598.2 link	c.162-43A>G	intron_variant	Intron 3 of 3		NP_001160070.1	Q6Q788A0A0B4RUS7
APOA5	NM_052968.5 link	c.162-43A>G	intron_variant	Intron 3 of 3		NP_443200.2	Q6Q788A0A0B4RUS7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
APOA5	ENST00000227665.9 link	c.162-43A>G		intron_variant	Intron 2 of 2	1	NM_001371904.1	ENSP00000227665.4	Q6Q788
APOA5	ENST00000433069.2 link	c.162-43A>G		intron_variant	Intron 3 of 3	1		ENSP00000399701.2	Q6Q788
APOA5	ENST00000673688.1 link	c.203A>G	p.Glu68Gly	missense_variant	Exon 3 of 3			ENSP00000501141.1	A0A669KB69
APOA5	ENST00000542499.5 link	c.162-43A>G		intron_variant	Intron 3 of 3	5		ENSP00000445002.1	Q6Q788

Frequencies

GnomAD3 genomes

AF:

0.934

AC:

142139

AN:

152202

Hom.:

66601

Cov.:

show subpopulations

Gnomad AFR

AF:

0.986

Gnomad AMI

AF:

0.931

Gnomad AMR

AF:

0.891

Gnomad ASJ

AF:

0.912

Gnomad EAS

AF:

0.769

Gnomad SAS

AF:

0.827

Gnomad FIN

AF:

0.920

Gnomad MID

AF:

0.896

Gnomad NFE

AF:

0.936

Gnomad OTH

AF:

0.922

GnomAD3 exomes

AF:

0.894

AC:

167051

AN:

186868

Hom.:

75077

AF XY:

0.893

AC XY:

92095

AN XY:

103144

show subpopulations

Gnomad AFR exome

AF:

0.989

Gnomad AMR exome

AF:

0.833

Gnomad ASJ exome

AF:

0.913

Gnomad EAS exome

AF:

0.784

Gnomad SAS exome

AF:

0.831

Gnomad FIN exome

AF:

0.919

Gnomad NFE exome

AF:

0.936

Gnomad OTH exome

AF:

0.913

GnomAD4 exome

AF:

0.924

AC:

1238710

AN:

1340582

Hom.:

573892

Cov.:

AF XY:

0.921

AC XY:

616835

AN XY:

669506

show subpopulations

Gnomad4 AFR exome

AF:

0.990

Gnomad4 AMR exome

AF:

0.839

Gnomad4 ASJ exome

AF:

0.912

Gnomad4 EAS exome

AF:

0.752

Gnomad4 SAS exome

AF:

0.832

Gnomad4 FIN exome

AF:

0.919

Gnomad4 NFE exome

AF:

0.940

Gnomad4 OTH exome

AF:

0.916

GnomAD4 genome

AF:

0.934

AC:

142244

AN:

152320

Hom.:

66650

Cov.:

AF XY:

0.930

AC XY:

69293

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.986

Gnomad4 AMR

AF:

0.891

Gnomad4 ASJ

AF:

0.912

Gnomad4 EAS

AF:

0.768

Gnomad4 SAS

AF:

0.827

Gnomad4 FIN

AF:

0.920

Gnomad4 NFE

AF:

0.936

Gnomad4 OTH

AF:

0.917

Alfa

AF:

0.933

Hom.:

12564

Bravo

AF:

0.934

Asia WGS

AF:

0.810

AC:

2819

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

- -

Aug 30, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 11588264) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.1

DANN

Benign

0.72

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over