Variant chr2-69044961-G-A 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.296+148G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0402 in 735,826 control chromosomes in the GnomAD database, including 806 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.034 ( 141 hom., cov: 32)

Exomes 𝑓: 0.042 ( 665 hom. )

Consequence

ANTXR1
NM_032208.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.27

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 2-69044961-G-A is Benign according to our data. Variant chr2-69044961-G-A is described in ClinVar as [Benign]. Clinvar id is 1276136.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANTXR1	NM_032208.3 link	c.296+148G>A		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.296+148G>A		intron_variant		1	NM_032208.3	ENSP00000301945.4		Q9H6X2-1

Frequencies

GnomAD3 genomes

AF:

0.0339

AC:

5156

AN:

152030

Hom.:

141

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00858

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0244

Gnomad ASJ

AF:

0.0406

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0563

Gnomad FIN

AF:

0.0960

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0431

Gnomad OTH

AF:

0.0268

GnomAD4 exome

AF:

0.0419

AC:

24434

AN:

583678

Hom.:

665

AF XY:

0.0431

AC XY:

13423

AN XY:

311592

show subpopulations

Gnomad4 AFR exome

AF:

0.00758

Gnomad4 AMR exome

AF:

0.0241

Gnomad4 ASJ exome

AF:

0.0488

Gnomad4 EAS exome

AF:

0.00125

Gnomad4 SAS exome

AF:

0.0557

Gnomad4 FIN exome

AF:

0.0822

Gnomad4 NFE exome

AF:

0.0423

Gnomad4 OTH exome

AF:

0.0388

GnomAD4 genome

AF:

0.0339

AC:

5161

AN:

152148

Hom.:

141

Cov.:

AF XY:

0.0367

AC XY:

2729

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.00855

Gnomad4 AMR

AF:

0.0245

Gnomad4 ASJ

AF:

0.0406

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0569

Gnomad4 FIN

AF:

0.0960

Gnomad4 NFE

AF:

0.0431

Gnomad4 OTH

AF:

0.0265

Alfa

AF:

0.0388

Hom.:

Bravo

AF:

0.0262

Asia WGS

AF:

0.0260

AC:

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

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 11, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

7.1

DANN

Benign

0.59

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