1-161223055-CCACACACA-C

Position:

• chr1-161223055-CCACACACA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001643.2(APOA2):​c.53-13_53-6del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0207 in 1,508,324 control chromosomes in the GnomAD database, including 31 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.010 (26 hom., cov: 0)
  • Exomes 𝑓: 0.022 (5 hom.)
• Consequence: APOA2 NM_001643.2 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 Benign. Variant got -10 ACMG points.

• BP6: Variant 1-161223055-CCACACACA-C is Benign according to our data. Variant chr1-161223055-CCACACACA-C is described in ClinVar as [Benign]. Clinvar id is 928702.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOA2	NM_001643.2	c.53-13_53-6del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000367990.7	NP_001634.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOA2	ENST00000367990.7	c.53-13_53-6del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_001643.2	ENSP00000356969	P1

Frequencies

GnomAD3 genomes AF: 0.0103 AC: 1513 AN: 147366 Hom.: 25 Cov.: 0

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00659

Gnomad ASJ AF: 0.000294

Gnomad EAS AF: 0.00585

Gnomad SAS AF: 0.00412

Gnomad FIN AF: 0.000711

Gnomad MID AF: 0.0192

Gnomad NFE AF: 0.00185

Gnomad OTH AF: 0.00938

GnomAD3 exomes AF: 0.0527 AC: 10309 AN: 195520 Hom.: 6 AF XY: 0.0530 AC XY: 5656 AN XY: 106664

Gnomad AFR exome AF: 0.0883

Gnomad AMR exome AF: 0.0569

Gnomad ASJ exome AF: 0.0401

Gnomad EAS exome AF: 0.0779

Gnomad SAS exome AF: 0.0612

Gnomad FIN exome AF: 0.0498

Gnomad NFE exome AF: 0.0424

Gnomad OTH exome AF: 0.0452

GnomAD4 exome AF: 0.0218 AC: 29652 AN: 1360850 Hom.: 5 AF XY: 0.0222 AC XY: 15024 AN XY: 677246

Gnomad4 AFR exome AF: 0.0627

Gnomad4 AMR exome AF: 0.0443

Gnomad4 ASJ exome AF: 0.0253

Gnomad4 EAS exome AF: 0.0550

Gnomad4 SAS exome AF: 0.0351

Gnomad4 FIN exome AF: 0.0331

Gnomad4 NFE exome AF: 0.0167

Gnomad4 OTH exome AF: 0.0262

GnomAD4 genome AF: 0.0103 AC: 1526 AN: 147474 Hom.: 26 Cov.: 0 AF XY: 0.0101 AC XY: 722 AN XY: 71650

Gnomad4 AFR AF: 0.0307

Gnomad4 AMR AF: 0.00658

Gnomad4 ASJ AF: 0.000294

Gnomad4 EAS AF: 0.00586

Gnomad4 SAS AF: 0.00391

Gnomad4 FIN AF: 0.000711

Gnomad4 NFE AF: 0.00185

Gnomad4 OTH AF: 0.00929

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Sep 20, 2019

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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;