2-69060811-A-G

Position:

• chr2-69060811-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000303714.9(ANTXR1):​c.297-9836A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,076 control chromosomes in the GnomAD database, including 18,463 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (18463 hom., cov: 32)
• Consequence: ANTXR1 ENST00000303714.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANTXR1	NM_032208.3	c.297-9836A>G		intron_variant		ENST00000303714.9	NP_115584.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANTXR1	ENST00000303714.9	c.297-9836A>G		intron_variant		1	NM_032208.3	ENSP00000301945	P1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60947 AN: 151958 Hom.: 18400 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.402 AC: 61067 AN: 152076 Hom.: 18463 Cov.: 32 AF XY: 0.406 AC XY: 30187 AN XY: 74330

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.349

Alfa AF: 0.204 Hom.: 9178

Bravo AF: 0.437

Asia WGS AF: 0.522 AC: 1813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.48

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: rs4315565; hg19: chr2-69287943;