1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACACACACACACACACA

Variant names:

• chr1-161223055-C-CCACACACA
• rs17244502
• NM_001643.2:c.53-13_53-6dupTGTGTGTG

Variant summary

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

The NM_001643.2(APOA2):​c.53-13_53-6dupTGTGTGTG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00064 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00034 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: APOA2 NM_001643.2 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

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 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOA2	NM_001643.2	c.53-13_53-6dupTGTGTGTG		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.53-13_53-6dupTGTGTGTG		splice_region_variant, intron_variant	Intron 2 of 3	1	NM_001643.2	ENSP00000356969.3
APOA2	ENST00000470459.6	c.53-13_53-6dupTGTGTGTG		splice_region_variant, intron_variant	Intron 2 of 4	5		ENSP00000477031.1

Frequencies

GnomAD3 genomes AF: 0.000637 AC: 94 AN: 147522 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000904

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00148

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000433

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000465

Gnomad OTH AF: 0.00148

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000337 AC: 485 AN: 1440376 Hom.: 0 Cov.: 0 AF XY: 0.000352 AC XY: 252 AN XY: 716634

Gnomad4 AFR exome AF: 0.000423

Gnomad4 AMR exome AF: 0.000682

Gnomad4 ASJ exome AF: 0.000194

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000949

Gnomad4 FIN exome AF: 0.0000208

Gnomad4 NFE exome AF: 0.000268

Gnomad4 OTH exome AF: 0.000638

GnomAD4 genome AF: 0.000637 AC: 94 AN: 147634 Hom.: 0 Cov.: 0 AF XY: 0.000669 AC XY: 48 AN XY: 71728

Gnomad4 AFR AF: 0.000926

Gnomad4 AMR AF: 0.00148

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000434

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000465

Gnomad4 OTH AF: 0.000977

Bravo AF: 0.000892

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;