2-69044974-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_032208.3(ANTXR1):c.296+161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0577 in 152,184 control chromosomes in the GnomAD database, including 284 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.058 (284 hom., cov: 32)
• Consequence: ANTXR1 NM_032208.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.60

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BP6: Variant 2-69044974-G-A is Benign according to our data. Variant chr2-69044974-G-A is described in ClinVar as [Benign]. Clinvar id is 1276091.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANTXR1	NM_032208.3	c.296+161G>A		intron_variant		ENST00000303714.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANTXR1	ENST00000303714.9	c.296+161G>A		intron_variant		1	NM_032208.3	P1

Frequencies

GnomAD3 genomes AF: 0.0577 AC: 8771 AN: 152064 Hom.: 282 Cov.: 32

Gnomad AFR AF: 0.0720

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.0481

Gnomad SAS AF: 0.0309

Gnomad FIN AF: 0.0196

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0593

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0577 AC: 8780 AN: 152184 Hom.: 284 Cov.: 32 AF XY: 0.0575 AC XY: 4275 AN XY: 74388

Gnomad4 AFR AF: 0.0720

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0504

Gnomad4 EAS AF: 0.0482

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.0196

Gnomad4 NFE AF: 0.0460

Gnomad4 OTH AF: 0.0573

Alfa AF: 0.0512 Hom.: 28

Bravo AF: 0.0679

Asia WGS AF: 0.0400 AC: 138 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	6.9
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

Other links and lift over

dbSNP: rs79295626; hg19: chr2-69272106;