Variant chr2-69040196-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032208.3(ANTXR1):c.224+81A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 1,253,810 control chromosomes in the GnomAD database, including 2,047 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.044 ( 189 hom., cov: 32)

Exomes 𝑓: 0.054 ( 1858 hom. )

Consequence

ANTXR1
NM_032208.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.124

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 2-69040196-A-G is Benign according to our data. Variant chr2-69040196-A-G is described in ClinVar as [Benign]. Clinvar id is 1226791.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANTXR1	NM_032208.3 link	c.224+81A>G		intron_variant		ENST00000303714.9	NP_115584.1	Q9H6X2-1Q53FL1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANTXR1	ENST00000303714.9 link	c.224+81A>G		intron_variant		1	NM_032208.3	ENSP00000301945.4		Q9H6X2-1

Frequencies

GnomAD3 genomes

AF:

0.0437

AC:

6658

AN:

152198

Hom.:

189

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0135

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.0565

Gnomad ASJ

AF:

0.0663

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0162

Gnomad FIN

AF:

0.0333

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0637

Gnomad OTH

AF:

0.0554

GnomAD4 exome

AF:

0.0537

AC:

59129

AN:

1101494

Hom.:

1858

AF XY:

0.0532

AC XY:

29858

AN XY:

561372

show subpopulations

Gnomad4 AFR exome

AF:

0.0146

Gnomad4 AMR exome

AF:

0.0417

Gnomad4 ASJ exome

AF:

0.0533

Gnomad4 EAS exome

AF:

0.000112

Gnomad4 SAS exome

AF:

0.0212

Gnomad4 FIN exome

AF:

0.0391

Gnomad4 NFE exome

AF:

0.0621

Gnomad4 OTH exome

AF:

0.0512

GnomAD4 genome

AF:

0.0437

AC:

6659

AN:

152316

Hom.:

189

Cov.:

AF XY:

0.0417

AC XY:

3104

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0134

Gnomad4 AMR

AF:

0.0564

Gnomad4 ASJ

AF:

0.0663

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0164

Gnomad4 FIN

AF:

0.0333

Gnomad4 NFE

AF:

0.0637

Gnomad4 OTH

AF:

0.0553

Alfa

AF:

0.0532

Hom.:

Bravo

AF:

0.0451

Asia WGS

AF:

0.00808

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -

GAPO syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

DANN

Benign

0.34

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