rs34590960

Variant names:

• chr2-69152482-G-A
• rs34590960
• NM_032208.3:c.1047+218G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-69152482-G-A
• chr2-69152482-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032208.3(ANTXR1):​c.1047+218G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 152,072 control chromosomes in the GnomAD database, including 16,167 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 0.45 (16167 hom., cov: 32)
• Consequence: ANTXR1 NM_032208.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• GAPO syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet, Ambry Genetics
• capillary infantile hemangioma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000300924 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANTXR1	NM_032208.3	c.1047+218G>A		intron_variant	Intron 13 of 17	ENST00000303714.9	NP_115584.1
ANTXR1	NM_053034.2	c.1047+218G>A		intron_variant	Intron 13 of 14		NP_444262.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANTXR1	ENST00000303714.9	c.1047+218G>A		intron_variant	Intron 13 of 17	1	NM_032208.3	ENSP00000301945.4
ANTXR1	ENST00000409349.7	c.1047+218G>A		intron_variant	Intron 13 of 14	1		ENSP00000386494.3
ANTXR1	ENST00000679548.1	c.888+218G>A		intron_variant	Intron 12 of 12			ENSP00000505578.1
ENSG00000300924	ENST00000775121.1	n.99+10607C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68308 AN: 151954 Hom.: 16158 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.449 AC: 68350 AN: 152072 Hom.: 16167 Cov.: 32 AF XY: 0.457 AC XY: 33941 AN XY: 74340

African (AFR) AF: 0.467 AC: 19395 AN: 41490

American (AMR) AF: 0.464 AC: 7088 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3470

East Asian (EAS) AF: 0.891 AC: 4608 AN: 5172

South Asian (SAS) AF: 0.665 AC: 3193 AN: 4804

European-Finnish (FIN) AF: 0.440 AC: 4651 AN: 10562

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26539 AN: 67970

Other (OTH) AF: 0.459 AC: 969 AN: 2110

Alfa AF: 0.403 Hom.: 8296

Bravo AF: 0.449

Asia WGS AF: 0.691 AC: 2400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.60
PhyloP100		0.087
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs34590960; hg19: chr2-69379614;