dbSNP rs1802932: ANXA11:p.Ile457Val (chr10-80157730-T-C) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_145868.2(ANXA11):c.1369A>G(p.Ile457Val) variant causes a missense change. The variant allele was found at a frequency of 0.0117 in 1,613,916 control chromosomes in the GnomAD database, including 149 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.0096 ( 19 hom., cov: 32)

Exomes 𝑓: 0.012 ( 130 hom. )

Consequence

ANXA11
NM_145868.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.98

Variant links:

Genes affected

ANXA11 (HGNC:535): (annexin A11) This gene encodes a member of the annexin family, a group of calcium-dependent phospholipid-binding proteins. Annexins have unique N-terminal domains and conserved C-terminal domains, which contain calcium-dependent phospholipid-binding sites. The encoded protein is a 56-kD antigen recognized by sera from patients with various autoimmune diseases. Several transcript variants encoding two different isoforms have been identified. [provided by RefSeq, Dec 2015]

ANXA11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007784903).

BP6

Variant 10-80157730-T-C is Benign according to our data. Variant chr10-80157730-T-C is described in ClinVar as [Benign]. Clinvar id is 718544.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 1467 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANXA11	NM_145868.2 link	c.1369A>G	p.Ile457Val	missense_variant	Exon 15 of 16	ENST00000422982.8	NP_665875.1	P50995-1Q5T0G8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANXA11	ENST00000422982.8 link	c.1369A>G	p.Ile457Val	missense_variant	Exon 15 of 16	1	NM_145868.2	ENSP00000404412.2		P50995-1

Frequencies

GnomAD3 genomes

AF:

0.00965

AC:

1467

AN:

152010

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00334

Gnomad ASJ

AF:

0.00375

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.0412

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0125

Gnomad OTH

AF:

0.00767

GnomAD3 exomes

AF:

0.00955

AC:

2401

AN:

251286

Hom.:

AF XY:

0.00957

AC XY:

1299

AN XY:

135806

show subpopulations

Gnomad AFR exome

AF:

0.00246

Gnomad AMR exome

AF:

0.00385

Gnomad ASJ exome

AF:

0.00528

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00121

Gnomad FIN exome

AF:

0.0340

Gnomad NFE exome

AF:

0.0118

Gnomad OTH exome

AF:

0.00962

GnomAD4 exome

AF:

0.0119

AC:

17462

AN:

1461788

Hom.:

130

Cov.:

AF XY:

0.0116

AC XY:

8405

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.00170

Gnomad4 AMR exome

AF:

0.00380

Gnomad4 ASJ exome

AF:

0.00479

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00139

Gnomad4 FIN exome

AF:

0.0307

Gnomad4 NFE exome

AF:

0.0132

Gnomad4 OTH exome

AF:

0.0111

GnomAD4 genome

AF:

0.00964

AC:

1467

AN:

152128

Hom.:

Cov.:

AF XY:

0.0104

AC XY:

775

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.00217

Gnomad4 AMR

AF:

0.00333

Gnomad4 ASJ

AF:

0.00375

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.0412

Gnomad4 NFE

AF:

0.0125

Gnomad4 OTH

AF:

0.00759

Alfa

AF:

0.0108

Hom.:

Bravo

AF:

0.00704

TwinsUK

AF:

0.0102

AC:

ALSPAC

AF:

0.0145

AC:

ESP6500AA

AF:

0.00295

AC:

ESP6500EA

AF:

0.0122

AC:

105

ExAC

AF:

0.00894

AC:

1086

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.0117

EpiControl

AF:

0.00978

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Nov 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ANXA11: BS1, BS2 -

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.015

T;T;.;T

Eigen

Benign

0.042

Eigen_PC

Benign

0.19

FATHMM_MKL

Uncertain

0.89

LIST_S2

Uncertain

0.87

.;.;D;D

MetaRNN

Benign

0.0078

T;T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.53

N;N;.;N

PrimateAI

Uncertain

0.71

PROVEAN

Benign

-0.37

N;N;.;N

REVEL

Benign

0.099

Sift

Benign

0.20

T;T;.;T

Sift4G

Benign

0.38

T;T;T;T

Polyphen

0.41

B;B;.;B

Vest4

0.15

MVP

0.20

MPC

0.14

ClinPred

0.014

GERP RS

5.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.16

gMVP

0.32

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over