rs1722784

chr1-150989393-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANXA9	NM_003568.3	c.852+1052A>G		intron_variant		ENST00000368947.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANXA9	ENST00000368947.9	c.852+1052A>G		intron_variant		1	NM_003568.3	P1

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

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.373

Alfa AF: 0.451 Hom.: 24876

Bravo AF: 0.344

Asia WGS AF: 0.212 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.8
Dann	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs1722784; hg19: chr1-150961869;