1-161223055-CCACACACACACACACACACACACA-CCACACACACA

Variant names:

• chr1-161223055-CCACACACACACACA-C
• rs17244502
• NM_001643.2:c.53-19_53-6delTGTGTGTGTGTGTG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001643.2(APOA2):​c.53-19_53-6delTGTGTGTGTGTGTG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00231 in 1,565,692 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00043 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0025 (0 hom.)
• Consequence: APOA2 NM_001643.2 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOA2	NM_001643.2	c.53-19_53-6delTGTGTGTGTGTGTG		splice_region_variant, intron_variant	Intron 2 of 3	ENST00000367990.7	NP_001634.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOA2	ENST00000367990.7	c.53-19_53-6delTGTGTGTGTGTGTG		splice_region_variant, intron_variant	Intron 2 of 3	1	NM_001643.2	ENSP00000356969.3
APOA2	ENST00000470459.6	c.53-19_53-6delTGTGTGTGTGTGTG		splice_region_variant, intron_variant	Intron 2 of 4	5		ENSP00000477031.1

Frequencies

GnomAD3 genomes AF: 0.000427 AC: 63 AN: 147516 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000753

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00101

Gnomad ASJ AF: 0.00588

Gnomad EAS AF: 0.000403

Gnomad SAS AF: 0.000217

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000285

Gnomad OTH AF: 0.00148

GnomAD3 exomes AF: 0.00977 AC: 1911 AN: 195520 Hom.: 1 AF XY: 0.00898 AC XY: 958 AN XY: 106664

Gnomad AFR exome AF: 0.00381

Gnomad AMR exome AF: 0.0156

Gnomad ASJ exome AF: 0.0179

Gnomad EAS exome AF: 0.0192

Gnomad SAS exome AF: 0.00547

Gnomad FIN exome AF: 0.00663

Gnomad NFE exome AF: 0.00830

Gnomad OTH exome AF: 0.00798

GnomAD4 exome AF: 0.00250 AC: 3547 AN: 1418064 Hom.: 0 AF XY: 0.00247 AC XY: 1746 AN XY: 705530

Gnomad4 AFR exome AF: 0.00125

Gnomad4 AMR exome AF: 0.0114

Gnomad4 ASJ exome AF: 0.0120

Gnomad4 EAS exome AF: 0.00907

Gnomad4 SAS exome AF: 0.00219

Gnomad4 FIN exome AF: 0.00378

Gnomad4 NFE exome AF: 0.00167

Gnomad4 OTH exome AF: 0.00318

GnomAD4 genome AF: 0.000427 AC: 63 AN: 147628 Hom.: 0 Cov.: 0 AF XY: 0.000349 AC XY: 25 AN XY: 71726

Gnomad4 AFR AF: 0.0000751

Gnomad4 AMR AF: 0.00101

Gnomad4 ASJ AF: 0.00588

Gnomad4 EAS AF: 0.000403

Gnomad4 SAS AF: 0.000217

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000285

Gnomad4 OTH AF: 0.00146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17244502; hg19: chr1-161192845;