Variant rs5085 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001643.2(APOA2):c.185+197G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,150 control chromosomes in the GnomAD database, including 2,264 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2264 hom., cov: 31)

Consequence

APOA2
NM_001643.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.725

Variant links:

Genes affected

APOA2 (HGNC:601): (apolipoprotein A2) This gene encodes apolipoprotein (apo-) A-II, which is the second most abundant protein of the high density lipoprotein particles. The protein is found in plasma as a monomer, homodimer, or heterodimer with apolipoprotein D. Defects in this gene may result in apolipoprotein A-II deficiency or hypercholesterolemia. [provided by RefSeq, Jul 2008]

APOA2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOA2	NM_001643.2 link	c.185+197G>C		intron_variant		ENST00000367990.7	NP_001634.1	P02652

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOA2	ENST00000367990.7 link	c.185+197G>C		intron_variant		1	NM_001643.2	ENSP00000356969.3		P02652
APOA2	ENST00000470459.6 link	c.185+197G>C		intron_variant		5		ENSP00000477031.1		V9GYS1

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

25008

AN:

152032

Hom.:

2265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.177

Gnomad OTH

AF:

0.175

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.164

AC:

24999

AN:

152150

Hom.:

2264

Cov.:

AF XY:

0.164

AC XY:

12200

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.220

Gnomad4 ASJ

AF:

0.218

Gnomad4 EAS

AF:

0.304

Gnomad4 SAS

AF:

0.136

Gnomad4 FIN

AF:

0.157

Gnomad4 NFE

AF:

0.177

Gnomad4 OTH

AF:

0.175

Alfa

AF:

0.164

Hom.:

290

Bravo

AF:

0.167

Asia WGS

AF:

0.246

AC:

853

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

8.7

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over