NM_032208.3:c.20G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032208.3(ANTXR1):c.20G>A(p.Arg7Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 1,588,742 control chromosomes in the GnomAD database, including 650 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 51 hom., cov: 32)

Exomes 𝑓: 0.011 ( 599 hom. )

Consequence

ANTXR1
NM_032208.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.648

Publications

9 publications found

Variant links:

Genes affected

ANTXR1 (HGNC:21014): (ANTXR cell adhesion molecule 1) This gene encodes a type I transmembrane protein and is a tumor-specific endothelial marker that has been implicated in colorectal cancer. The encoded protein has been shown to also be a docking protein or receptor for Bacillus anthracis toxin, the causative agent of the disease, anthrax. The binding of the protective antigen (PA) component, of the tripartite anthrax toxin, to this receptor protein mediates delivery of toxin components to the cytosol of cells. Once inside the cell, the other two components of anthrax toxin, edema factor (EF) and lethal factor (LF) disrupt normal cellular processes. Three alternatively spliced variants that encode different protein isoforms have been described. [provided by RefSeq, Oct 2008]

ANTXR1 Gene-Disease associations (from GenCC):

GAPO syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)
capillary infantile hemangioma
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ANTXR1 links:

ENSG00000300948 (HGNC:):

ENSG00000300948 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0014003515).

BP6

Variant 2-69013519-G-A is Benign according to our data. Variant chr2-69013519-G-A is described in ClinVar as Benign. ClinVar VariationId is 1180103.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032208.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ANTXR1	NM_032208.3	MANE Select	c.20G>A	p.Arg7Lys	missense	Exon 1 of 18	NP_115584.1	Q9H6X2-1
ANTXR1	NM_053034.2		c.20G>A	p.Arg7Lys	missense	Exon 1 of 15	NP_444262.1	Q9H6X2-2
ANTXR1	NM_001410840.1		c.20G>A	p.Arg7Lys	missense	Exon 1 of 13	NP_001397769.1	H0YC24

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ANTXR1	ENST00000303714.9	TSL:1 MANE Select	c.20G>A	p.Arg7Lys	missense	Exon 1 of 18	ENSP00000301945.4	Q9H6X2-1
ANTXR1	ENST00000409349.7	TSL:1	c.20G>A	p.Arg7Lys	missense	Exon 1 of 15	ENSP00000386494.3	Q9H6X2-2
ANTXR1	ENST00000409829.7	TSL:1	c.20G>A	p.Arg7Lys	missense	Exon 1 of 13	ENSP00000387058.3	Q9H6X2-4

Frequencies

GnomAD3 genomes

AF:

0.0114

AC:

1742

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000506

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0130

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.0501

Gnomad FIN

AF:

0.0461

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00243

Gnomad OTH

AF:

0.00525

GnomAD2 exomes

AF:

0.0245

AC:

5024

AN:

205318

AF XY:

0.0242

show subpopulations

Gnomad AFR exome

AF:

0.000558

Gnomad AMR exome

AF:

0.0256

Gnomad ASJ exome

AF:

0.0115

Gnomad EAS exome

AF:

0.117

Gnomad FIN exome

AF:

0.0447

Gnomad NFE exome

AF:

0.00295

Gnomad OTH exome

AF:

0.0136

GnomAD4 exome

AF:

0.0106

AC:

15160

AN:

1436402

Hom.:

599

Cov.:

AF XY:

0.0114

AC XY:

8115

AN XY:

711692

show subpopulations

African (AFR)

AF:

0.000360

AC:

AN:

33368

American (AMR)

AF:

0.0245

AC:

967

AN:

39478

Ashkenazi Jewish (ASJ)

AF:

0.0138

AC:

352

AN:

25528

East Asian (EAS)

AF:

0.136

AC:

5263

AN:

38830

South Asian (SAS)

AF:

0.0472

AC:

3860

AN:

81704

European-Finnish (FIN)

AF:

0.0424

AC:

2182

AN:

51508

Middle Eastern (MID)

AF:

0.00503

AC:

AN:

4966

European-Non Finnish (NFE)

AF:

0.00161

AC:

1774

AN:

1101470

Other (OTH)

AF:

0.0122

AC:

725

AN:

59550

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

989

1979

2968

3958

4947

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

172

344

516

688

860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0114

AC:

1744

AN:

152340

Hom.:

Cov.:

AF XY:

0.0148

AC XY:

1103

AN XY:

74486

show subpopulations

African (AFR)

AF:

0.000505

AC:

AN:

41586

American (AMR)

AF:

0.0132

AC:

202

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0130

AC:

AN:

3468

East Asian (EAS)

AF:

0.109

AC:

567

AN:

5180

South Asian (SAS)

AF:

0.0501

AC:

242

AN:

4830

European-Finnish (FIN)

AF:

0.0461

AC:

489

AN:

10618

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00243

AC:

165

AN:

68026

Other (OTH)

AF:

0.00520

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

173

260

346

433

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00840

Hom.:

Bravo

AF:

0.00860

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00311

AC:

ESP6500AA

AF:

0.000457

AC:

ESP6500EA

AF:

0.00222

AC:

ExAC

AF:

0.0193

AC:

2289

Asia WGS

AF:

0.0710

AC:

247

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

ANTXR1-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

(source)

DANN

Benign

0.86

DEOGEN2

Benign

0.062

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.11

LIST_S2

Benign

0.57

MetaRNN

Benign

0.0014

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.90

PhyloP100

0.65

PrimateAI

Benign

0.26

PROVEAN

Benign

-0.47

REVEL

Benign

0.035

Sift

Benign

0.39

Sift4G

Benign

0.18

Polyphen

0.0

Vest4

0.022

MPC

0.90

ClinPred

0.0029

GERP RS

-2.8

PromoterAI

0.041

Neutral

(source)

Varity_R

0.046

gMVP

0.40

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over