rs855523

Positions:

• chr9-33624431-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_003573.1(ANXA2P2):​n.207A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.101 in 1,609,790 control chromosomes in the GnomAD database, including 9,096 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 0.11 (1194 hom., cov: 32)
  • Exomes 𝑓: 0.099 (7902 hom.)
• Consequence: ANXA2P2 NR_003573.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.99

Genes affected

ANXA2P2 (HGNC:539): (annexin A2 pseudogene 2) Predicted to enable several functions, including phospholipase A2 inhibitor activity; phospholipid binding activity; and virion binding activity. Predicted to be involved in calcium ion transmembrane transport and negative regulation of catalytic activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANXA2P2	NR_003573.1	n.207A>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANXA2P2	ENST00000435128.2	n.158A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17376 AN: 152018 Hom.: 1185 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.0623

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0854

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.110

GnomAD3 exomes AF: 0.0996 AC: 25047 AN: 251450 Hom.: 1514 AF XY: 0.102 AC XY: 13826 AN XY: 135894

Gnomad AFR exome AF: 0.183

Gnomad AMR exome AF: 0.0509

Gnomad ASJ exome AF: 0.0951

Gnomad EAS exome AF: 0.0639

Gnomad SAS exome AF: 0.171

Gnomad FIN exome AF: 0.0875

Gnomad NFE exome AF: 0.0919

Gnomad OTH exome AF: 0.0976

GnomAD4 exome AF: 0.0991 AC: 144437 AN: 1457652 Hom.: 7902 Cov.: 31 AF XY: 0.101 AC XY: 73052 AN XY: 725448

Gnomad4 AFR exome AF: 0.188

Gnomad4 AMR exome AF: 0.0536

Gnomad4 ASJ exome AF: 0.0914

Gnomad4 EAS exome AF: 0.0735

Gnomad4 SAS exome AF: 0.166

Gnomad4 FIN exome AF: 0.0894

Gnomad4 NFE exome AF: 0.0943

Gnomad4 OTH exome AF: 0.101

GnomAD4 genome AF: 0.114 AC: 17409 AN: 152138 Hom.: 1194 Cov.: 32 AF XY: 0.115 AC XY: 8530 AN XY: 74376

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0662

Gnomad4 ASJ AF: 0.0939

Gnomad4 EAS AF: 0.0624

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0854

Gnomad4 NFE AF: 0.0911

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0921 Hom.: 1052

Bravo AF: 0.114

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs855523; hg19: chr9-33624429; COSMIC: COSV59346871;