Variant chr11-116791863-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001371904.1(APOA5):c.-3G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.913 in 1,614,018 control chromosomes in the GnomAD database, including 675,649 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.89 ( 60477 hom., cov: 34)

Exomes 𝑓: 0.92 ( 615172 hom. )

Consequence

APOA5
NM_001371904.1 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.137

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=-0.85).

BP6

Variant 11-116791863-C-T is Benign according to our data. Variant chr11-116791863-C-T is described in ClinVar as [Benign]. Clinvar id is 1284811.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-116791863-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
APOA5	NM_001371904.1 linkuse as main transcript	c.-3G>A	5_prime_UTR_variant	1/3	ENST00000227665.9	NP_001358833.1
APOA5	NM_001166598.2 linkuse as main transcript	c.-3G>A	5_prime_UTR_variant	2/4		NP_001160070.1
APOA5	NM_052968.5 linkuse as main transcript	c.-3G>A	5_prime_UTR_variant	2/4		NP_443200.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
APOA5	ENST00000227665.9 linkuse as main transcript	c.-3G>A	5_prime_UTR_variant	1/3	1	NM_001371904.1	ENSP00000227665	P1
APOA5	ENST00000433069.2 linkuse as main transcript	c.-3G>A	5_prime_UTR_variant	2/4	1		ENSP00000399701	P1
APOA5	ENST00000542499.5 linkuse as main transcript	c.-3G>A	5_prime_UTR_variant	2/4	5		ENSP00000445002	P1
APOA5	ENST00000673688.1 linkuse as main transcript	c.-3G>A	5_prime_UTR_variant	1/3			ENSP00000501141

Frequencies

GnomAD3 genomes

AF:

0.890

AC:

135380

AN:

152184

Hom.:

60460

Cov.:

show subpopulations

Gnomad AFR

AF:

0.849

Gnomad AMI

AF:

0.933

Gnomad AMR

AF:

0.864

Gnomad ASJ

AF:

0.897

Gnomad EAS

AF:

0.700

Gnomad SAS

AF:

0.811

Gnomad FIN

AF:

0.920

Gnomad MID

AF:

0.880

Gnomad NFE

AF:

0.934

Gnomad OTH

AF:

0.884

GnomAD3 exomes

AF:

0.879

AC:

220186

AN:

250512

Hom.:

97522

AF XY:

0.881

AC XY:

119421

AN XY:

135580

show subpopulations

Gnomad AFR exome

AF:

0.848

Gnomad AMR exome

AF:

0.820

Gnomad ASJ exome

AF:

0.899

Gnomad EAS exome

AF:

0.715

Gnomad SAS exome

AF:

0.818

Gnomad FIN exome

AF:

0.918

Gnomad NFE exome

AF:

0.934

Gnomad OTH exome

AF:

0.901

GnomAD4 exome

AF:

0.916

AC:

1338287

AN:

1461716

Hom.:

615172

Cov.:

AF XY:

0.913

AC XY:

663959

AN XY:

727154

show subpopulations

Gnomad4 AFR exome

AF:

0.842

Gnomad4 AMR exome

AF:

0.825

Gnomad4 ASJ exome

AF:

0.898

Gnomad4 EAS exome

AF:

0.679

Gnomad4 SAS exome

AF:

0.819

Gnomad4 FIN exome

AF:

0.918

Gnomad4 NFE exome

AF:

0.939

Gnomad4 OTH exome

AF:

0.901

GnomAD4 genome

AF:

0.889

AC:

135451

AN:

152302

Hom.:

60477

Cov.:

AF XY:

0.886

AC XY:

66012

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.849

Gnomad4 AMR

AF:

0.864

Gnomad4 ASJ

AF:

0.897

Gnomad4 EAS

AF:

0.699

Gnomad4 SAS

AF:

0.811

Gnomad4 FIN

AF:

0.920

Gnomad4 NFE

AF:

0.934

Gnomad4 OTH

AF:

0.879

Alfa

AF:

0.922

Hom.:

139825

Bravo

AF:

0.884

Asia WGS

AF:

0.766

AC:

2665

AN:

3478

EpiCase

AF:

0.928

EpiControl

AF:

0.927

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 07, 2023	- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.4

DANN

Benign

0.76

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