9-33624431-A-C

Variant names:

• chr9-33624431-A-C
• rs855523
• ENST00000435128.2:n.158A>C

Variant summary

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

The ENST00000435128.2(ANXA2P2):​n.158A>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 ENST00000435128.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.99
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435128.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANXA2P2	NR_003573.1		n.207A>C		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANXA2P2	ENST00000435128.2	TSL:6	n.158A>C		non_coding_transcript_exon	Exon 1 of 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

GnomAD2 exomes AF: 0.0996 AC: 25047 AN: 251450 AF XY: 0.102

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 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

African (AFR) AF: 0.188 AC: 6282 AN: 33392

American (AMR) AF: 0.0536 AC: 2398 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 2388 AN: 26114

East Asian (EAS) AF: 0.0735 AC: 2917 AN: 39674

South Asian (SAS) AF: 0.166 AC: 14308 AN: 86162

European-Finnish (FIN) AF: 0.0894 AC: 4776 AN: 53418

Middle Eastern (MID) AF: 0.143 AC: 825 AN: 5766

European-Non Finnish (NFE) AF: 0.0943 AC: 104446 AN: 1108132

Other (OTH) AF: 0.101 AC: 6097 AN: 60276

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

African (AFR) AF: 0.183 AC: 7590 AN: 41462

American (AMR) AF: 0.0662 AC: 1012 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0939 AC: 326 AN: 3470

East Asian (EAS) AF: 0.0624 AC: 323 AN: 5174

South Asian (SAS) AF: 0.162 AC: 781 AN: 4824

European-Finnish (FIN) AF: 0.0854 AC: 905 AN: 10594

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0911 AC: 6193 AN: 68000

Other (OTH) AF: 0.108 AC: 228 AN: 2112

Alfa AF: 0.0954 Hom.: 2325

Bravo AF: 0.114

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.6
DANN	Benign	0.61
PhyloP100		6.0

Splicing

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

Other links and lift over

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