chr1-150990447-G-A

Position:

• chr1-150990447-G-A

Variant summary

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

The NM_003568.3(ANXA9):​c.852+2106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,638 control chromosomes in the GnomAD database, including 27,798 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 0.60 (27798 hom., cov: 31)
• Consequence: ANXA9 NM_003568.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANXA9	NM_003568.3	c.852+2106G>A		intron_variant		ENST00000368947.9	NP_003559.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANXA9	ENST00000368947.9	c.852+2106G>A		intron_variant		1	NM_003568.3	ENSP00000357943	P1

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90130 AN: 151518 Hom.: 27754 Cov.: 31

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.595 AC: 90231 AN: 151638 Hom.: 27798 Cov.: 31 AF XY: 0.596 AC XY: 44127 AN XY: 74050

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.599

Alfa AF: 0.549 Hom.: 2787

Bravo AF: 0.610

Asia WGS AF: 0.779 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.51

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: rs11204756; hg19: chr1-150962923;