rs5082

Variant names:

• chr1-161223893-G-A
• rs5082
• ENST00000888433.1:c.-25+367C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-161223893-G-A
• chr1-161223893-G-C
• chr1-161223893-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000888433.1(APOA2):​c.-25+367C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 151,986 control chromosomes in the GnomAD database, including 35,682 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: 𝑓 0.68 (35682 hom., cov: 30)
• Consequence: APOA2 ENST00000888433.1 intron
• Clinical Significance: Uncertain significance criteria provided, single submitter P:1 U:1
• Conservation: PhyloP100: 0.00100
• Publications: 147 publications found

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 Gene-Disease associations (from GenCC):

• apolipoprotein A-II amyloidosis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000888433.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOA2	ENST00000888433.1		c.-25+367C>T		intron	N/A	ENSP00000558492.1
	APOA2	ENST00000888434.1		c.-25+83C>T		intron	N/A	ENSP00000558493.1
	APOA2	ENST00000888435.1		c.-259C>T		upstream_gene	N/A	ENSP00000558494.1

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103182 AN: 151868 Hom.: 35628 Cov.: 30

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.680 AC: 103295 AN: 151986 Hom.: 35682 Cov.: 30 AF XY: 0.683 AC XY: 50708 AN XY: 74288

African (AFR) AF: 0.769 AC: 31853 AN: 41436

American (AMR) AF: 0.711 AC: 10856 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2146 AN: 3472

East Asian (EAS) AF: 0.908 AC: 4698 AN: 5172

South Asian (SAS) AF: 0.749 AC: 3607 AN: 4818

European-Finnish (FIN) AF: 0.621 AC: 6555 AN: 10564

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41451 AN: 67940

Other (OTH) AF: 0.668 AC: 1413 AN: 2114

Alfa AF: 0.637 Hom.: 120136

Bravo AF: 0.694

Asia WGS AF: 0.836 AC: 2900 AN: 3478

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	Apolipoprotein A-II amyloidosis (1)
1	-	-	Hypercholesterolemia, familial, 1 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.36
PhyloP100		0.0010
PromoterAI		-0.0068	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5082; hg19: chr1-161193683;