Variant 2-69013740-G-C 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.152+89G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 1,546,888 control chromosomes in the GnomAD database, including 1,890 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.037 ( 173 hom., cov: 32)

Exomes 𝑓: 0.047 ( 1717 hom. )

Consequence

ANTXR1
NM_032208.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.24

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=-0.79).

BP6

Variant 2-69013740-G-C is Benign according to our data. Variant chr2-69013740-G-C is described in ClinVar as [Benign]. Clinvar id is 1221510.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANTXR1	NM_032208.3 link	c.152+89G>C		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.152+89G>C		intron_variant		1	NM_032208.3	ENSP00000301945.4		Q9H6X2-1

Frequencies

GnomAD3 genomes

AF:

0.0374

AC:

5686

AN:

152220

Hom.:

173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00859

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0553

Gnomad ASJ

AF:

0.0412

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0544

Gnomad FIN

AF:

0.0960

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0438

Gnomad OTH

AF:

0.0316

GnomAD4 exome

AF:

0.0466

AC:

64957

AN:

1394550

Hom.:

1717

AF XY:

0.0466

AC XY:

32092

AN XY:

688084

show subpopulations

Gnomad4 AFR exome

AF:

0.00620

Gnomad4 AMR exome

AF:

0.0683

Gnomad4 ASJ exome

AF:

0.0495

Gnomad4 EAS exome

AF:

0.000728

Gnomad4 SAS exome

AF:

0.0518

Gnomad4 FIN exome

AF:

0.0874

Gnomad4 NFE exome

AF:

0.0465

Gnomad4 OTH exome

AF:

0.0436

GnomAD4 genome

AF:

0.0374

AC:

5694

AN:

152338

Hom.:

173

Cov.:

AF XY:

0.0401

AC XY:

2989

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.00856

Gnomad4 AMR

AF:

0.0554

Gnomad4 ASJ

AF:

0.0412

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0553

Gnomad4 FIN

AF:

0.0960

Gnomad4 NFE

AF:

0.0438

Gnomad4 OTH

AF:

0.0313

Alfa

AF:

0.0407

Hom.:

Bravo

AF:

0.0327

Asia WGS

AF:

0.0240

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 11, 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

-0.79

CADD

Benign

DANN

Benign

0.69

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