NM_003568.3:c.852+1052A>G

Variant names:

• chr1-150989393-A-G
• rs1722784
• NM_003568.3:c.852+1052A>G

Variant summary

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

The NM_003568.3(ANXA9):​c.852+1052A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,788 control chromosomes in the GnomAD database, including 11,947 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 0.36 (11947 hom., cov: 29)
• Consequence: ANXA9 NM_003568.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 25 publications found

Genes affected

ANXA9 (HGNC:547): (annexin A9) The annexins are a family of calcium-dependent phospholipid-binding proteins. Members of the annexin family contain 4 internal repeat domains, each of which includes a type II calcium-binding site. The calcium-binding sites are required for annexins to aggregate and cooperatively bind anionic phospholipids and extracellular matrix proteins. This gene encodes a divergent member of the annexin protein family in which all four homologous type II calcium-binding sites in the conserved tetrad core contain amino acid substitutions that ablate their function. However, structural analysis suggests that the conserved putative ion channel formed by the tetrad core is intact. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003568.3. 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
	ANXA9	NM_003568.3	MANE Select	c.852+1052A>G		intron	N/A	NP_003559.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANXA9	ENST00000368947.9	TSL:1 MANE Select	c.852+1052A>G		intron	N/A	ENSP00000357943.4

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55272 AN: 151670 Hom.: 11949 Cov.: 29

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.377

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.364 AC: 55268 AN: 151788 Hom.: 11947 Cov.: 29 AF XY: 0.365 AC XY: 27050 AN XY: 74136

African (AFR) AF: 0.151 AC: 6266 AN: 41454

American (AMR) AF: 0.371 AC: 5659 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1099 AN: 3460

East Asian (EAS) AF: 0.151 AC: 775 AN: 5146

South Asian (SAS) AF: 0.246 AC: 1182 AN: 4798

European-Finnish (FIN) AF: 0.555 AC: 5819 AN: 10480

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 32991 AN: 67888

Other (OTH) AF: 0.373 AC: 785 AN: 2104

Alfa AF: 0.429 Hom.: 35078

Bravo AF: 0.344

Asia WGS AF: 0.212 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.65
PhyloP100		0.059
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1722784; hg19: chr1-150961869;