Variant chr1-150986360-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000368947.9(ANXA9):c.497A>G(p.Asp166Gly) variant causes a missense change. The variant allele was found at a frequency of 0.142 in 1,613,636 control chromosomes in the GnomAD database, including 17,620 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.12 ( 1227 hom., cov: 32)

Exomes 𝑓: 0.14 ( 16393 hom. )

Consequence

ANXA9
ENST00000368947.9 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.90

Variant links:

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]

ANXA9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0023424923).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANXA9	NM_003568.3 linkuse as main transcript	c.497A>G	p.Asp166Gly	missense_variant	8/14	ENST00000368947.9	NP_003559.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANXA9	ENST00000368947.9 linkuse as main transcript	c.497A>G	p.Asp166Gly	missense_variant	8/14	1	NM_003568.3	ENSP00000357943	P1

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17805

AN:

152098

Hom.:

1227

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0610

Gnomad AMI

AF:

0.274

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.0262

Gnomad SAS

AF:

0.0625

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.128

GnomAD3 exomes

AF:

0.118

AC:

29474

AN:

250636

Hom.:

2036

AF XY:

0.118

AC XY:

15977

AN XY:

135458

show subpopulations

Gnomad AFR exome

AF:

0.0567

Gnomad AMR exome

AF:

0.0790

Gnomad ASJ exome

AF:

0.167

Gnomad EAS exome

AF:

0.0341

Gnomad SAS exome

AF:

0.0714

Gnomad FIN exome

AF:

0.141

Gnomad NFE exome

AF:

0.154

Gnomad OTH exome

AF:

0.138

GnomAD4 exome

AF:

0.145

AC:

211818

AN:

1461420

Hom.:

16393

Cov.:

AF XY:

0.143

AC XY:

104304

AN XY:

727032

show subpopulations

Gnomad4 AFR exome

AF:

0.0545

Gnomad4 AMR exome

AF:

0.0810

Gnomad4 ASJ exome

AF:

0.167

Gnomad4 EAS exome

AF:

0.0426

Gnomad4 SAS exome

AF:

0.0724

Gnomad4 FIN exome

AF:

0.145

Gnomad4 NFE exome

AF:

0.159

Gnomad4 OTH exome

AF:

0.136

GnomAD4 genome

AF:

0.117

AC:

17801

AN:

152216

Hom.:

1227

Cov.:

AF XY:

0.115

AC XY:

8587

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.0608

Gnomad4 AMR

AF:

0.100

Gnomad4 ASJ

AF:

0.174

Gnomad4 EAS

AF:

0.0259

Gnomad4 SAS

AF:

0.0628

Gnomad4 FIN

AF:

0.141

Gnomad4 NFE

AF:

0.157

Gnomad4 OTH

AF:

0.127

Alfa

AF:

0.145

Hom.:

4390

Bravo

AF:

0.112

TwinsUK

AF:

0.158

AC:

586

ALSPAC

AF:

0.145

AC:

559

ESP6500AA

AF:

0.0615

AC:

271

ESP6500EA

AF:

0.155

AC:

1332

ExAC

AF:

0.116

AC:

14133

Asia WGS

AF:

0.0470

AC:

166

AN:

3478

EpiCase

AF:

0.158

EpiControl

AF:

0.155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.55

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.43

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.085

Eigen

Uncertain

0.63

Eigen_PC

Uncertain

0.51

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.74

MetaRNN

Benign

0.0023

MetaSVM

Benign

-1.0

MutationAssessor

Pathogenic

4.2

MutationTaster

Benign

0.0027

PrimateAI

Benign

0.46

PROVEAN

Uncertain

-4.0

REVEL

Benign

0.17

Sift

Uncertain

0.016

Sift4G

Uncertain

0.058

Polyphen

0.99

Vest4

0.27

MPC

0.39

ClinPred

0.042

GERP RS

5.1

Varity_R

0.80

gMVP

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over