Variant 19-44948390-C-G 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_000483.5(APOC2):c.-13-76C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0161 in 1,266,596 control chromosomes in the GnomAD database, including 597 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.039 ( 267 hom., cov: 32)

Exomes 𝑓: 0.013 ( 330 hom. )

Consequence

APOC2
NM_000483.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.42

Variant links:

Genes affected

APOC2 (HGNC:609): (apolipoprotein C2) This gene encodes a lipid-binding protein belonging to the apolipoprotein gene family. The protein is secreted in plasma where it is a component of very low density lipoprotein. This protein activates the enzyme lipoprotein lipase, which hydrolyzes triglycerides and thus provides free fatty acids for cells. Mutations in this gene cause hyperlipoproteinemia type IB, characterized by hypertriglyceridemia, xanthomas, and increased risk of pancreatitis and early atherosclerosis. This gene is present in a cluster with other related apolipoprotein genes on chromosome 19. Naturally occurring read-through transcription exists between this gene and the neighboring upstream apolipoprotein C-IV (APOC4) gene. [provided by RefSeq, Mar 2011]

APOC2 links:

APOC4-APOC2 (HGNC:):

APOC4-APOC2 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=-0.91).

BP6

Variant 19-44948390-C-G is Benign according to our data. Variant chr19-44948390-C-G is described in ClinVar as [Benign]. Clinvar id is 1268118.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-44948390-C-G is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOC2	NM_000483.5 linkuse as main transcript	c.-13-76C>G		intron_variant		ENST00000252490.7
APOC4-APOC2	NR_037932.1 linkuse as main transcript	n.1195-76C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOC2	ENST00000252490.7 linkuse as main transcript	c.-13-76C>G		intron_variant		2	NM_000483.5	P1

Frequencies

GnomAD3 genomes

AF:

0.0390

AC:

5924

AN:

152074

Hom.:

267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0191

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0535

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00907

Gnomad OTH

AF:

0.0311

GnomAD4 exome

AF:

0.0130

AC:

14513

AN:

1114404

Hom.:

330

Cov.:

AF XY:

0.0140

AC XY:

7991

AN XY:

569982

show subpopulations

Gnomad4 AFR exome

AF:

0.112

Gnomad4 AMR exome

AF:

0.0110

Gnomad4 ASJ exome

AF:

0.00326

Gnomad4 EAS exome

AF:

0.0000263

Gnomad4 SAS exome

AF:

0.0482

Gnomad4 FIN exome

AF:

0.00293

Gnomad4 NFE exome

AF:

0.00772

Gnomad4 OTH exome

AF:

0.0165

GnomAD4 genome

AF:

0.0390

AC:

5937

AN:

152192

Hom.:

267

Cov.:

AF XY:

0.0384

AC XY:

2858

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.113

Gnomad4 AMR

AF:

0.0190

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0533

Gnomad4 FIN

AF:

0.00151

Gnomad4 NFE

AF:

0.00907

Gnomad4 OTH

AF:

0.0307

Alfa

AF:

0.00816

Hom.:

Bravo

AF:

0.0425

Asia WGS

AF:

0.0190

AC:

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

Oct 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.16

DANN

Benign

0.45

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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