Variant 11-116790097-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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, single submitter B:1

Conservation

PhyloP100: -0.411

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 -14 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 id is 1293389.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-116790097-G-A is described in Lovd as [Benign].

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/exons	MANE
APOA5	NM_001371904.1 linkuse as main transcript	c.*31C>T	3_prime_UTR_variant	3/3	ENST00000227665.9
APOA5	NM_001166598.2 linkuse as main transcript	c.*31C>T	3_prime_UTR_variant	4/4
APOA5	NM_052968.5 linkuse as main transcript	c.*31C>T	3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
APOA5	ENST00000227665.9 linkuse as main transcript	c.*31C>T	3_prime_UTR_variant	3/3	1	NM_001371904.1	P1
APOA5	ENST00000433069.2 linkuse as main transcript	c.*31C>T	3_prime_UTR_variant	4/4	1		P1
APOA5	ENST00000542499.5 linkuse as main transcript	c.*31C>T	3_prime_UTR_variant	4/4	5		P1
APOA5	ENST00000673688.1 linkuse as main transcript	c.*31C>T	3_prime_UTR_variant	3/3

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

GnomAD3 exomes

AF:

0.189

AC:

45691

AN:

241740

Hom.:

4918

AF XY:

0.194

AC XY:

25371

AN XY:

130916

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 SAS exome

AF:

0.144

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

Gnomad4 AFR exome

AF:

0.114

Gnomad4 AMR exome

AF:

0.134

Gnomad4 ASJ exome

AF:

0.258

Gnomad4 EAS exome

AF:

0.000939

Gnomad4 SAS exome

AF:

0.146

Gnomad4 FIN exome

AF:

0.223

Gnomad4 NFE exome

AF:

0.246

Gnomad4 OTH exome

AF:

0.217

GnomAD4 genome

AF:

0.192

AC:

29162

AN:

152222

Hom.:

3246

Cov.:

AF XY:

0.189

AC XY:

14035

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.118

Gnomad4 AMR

AF:

0.171

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.00367

Gnomad4 SAS

AF:

0.131

Gnomad4 FIN

AF:

0.222

Gnomad4 NFE

AF:

0.251

Gnomad4 OTH

AF:

0.202

Alfa

AF:

0.241

Hom.:

4174

Bravo

AF:

0.182

Asia WGS

AF:

0.0720

AC:

250

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

Cadd

Benign

7.7

Dann

Benign

0.75

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