10-64826548-A-G

Variant names:

• chr10-64826548-A-G
• rs1227236
• ENST00000404883.2:n.977A>G

Variant summary

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

The ENST00000404883.2(ANXA2P3):​n.977A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 726,584 control chromosomes in the GnomAD database, including 150,368 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 0.67 (35119 hom., cov: 32)
  • Exomes 𝑓: 0.63 (115249 hom.)
• Consequence: ANXA2P3 ENST00000404883.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.34
• Publications: 5 publications found

Genes affected

ANXA2P3 (HGNC:540): (annexin A2 pseudogene 3)

ENSG00000293732 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANXA2P3	NR_001446.2	n.1021A>G		non_coding_transcript_exon_variant	Exon 1 of 1
LOC105378336	XR_946020.2	n.49+11546A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANXA2P3	ENST00000404883.2	n.977A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000293732	ENST00000718642.1	n.195+11546A>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102459 AN: 151920 Hom.: 35073 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.660

GnomAD4 exome AF: 0.632 AC: 362984 AN: 574546 Hom.: 115249 Cov.: 0 AF XY: 0.630 AC XY: 198719 AN XY: 315232

African (AFR) AF: 0.801 AC: 13112 AN: 16376

American (AMR) AF: 0.687 AC: 28707 AN: 41780

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 11602 AN: 19224

East Asian (EAS) AF: 0.579 AC: 19027 AN: 32848

South Asian (SAS) AF: 0.650 AC: 44756 AN: 68838

European-Finnish (FIN) AF: 0.607 AC: 25489 AN: 41974

Middle Eastern (MID) AF: 0.625 AC: 2440 AN: 3904

European-Non Finnish (NFE) AF: 0.622 AC: 198973 AN: 319942

Other (OTH) AF: 0.636 AC: 18878 AN: 29660

GnomAD4 genome AF: 0.675 AC: 102560 AN: 152038 Hom.: 35119 Cov.: 32 AF XY: 0.672 AC XY: 49893 AN XY: 74280

African (AFR) AF: 0.801 AC: 33253 AN: 41508

American (AMR) AF: 0.693 AC: 10576 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2157 AN: 3468

East Asian (EAS) AF: 0.596 AC: 3066 AN: 5144

South Asian (SAS) AF: 0.640 AC: 3086 AN: 4822

European-Finnish (FIN) AF: 0.588 AC: 6199 AN: 10548

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.617 AC: 41953 AN: 67978

Other (OTH) AF: 0.657 AC: 1386 AN: 2110

Alfa AF: 0.636 Hom.: 39163

Bravo AF: 0.688

Asia WGS AF: 0.636 AC: 2217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.5
DANN	Benign	0.39
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs1227236; hg19: chr10-66586305;