chr2-69013206-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_032208.3(ANTXR1):c.-294G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 471,478 control chromosomes in the GnomAD database, including 384 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.035 ( 312 hom., cov: 31)
Exomes 𝑓: 0.0049 ( 72 hom. )
Consequence
ANTXR1
NM_032208.3 5_prime_UTR
NM_032208.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.256
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 2-69013206-G-A is Benign according to our data. Variant chr2-69013206-G-A is described in ClinVar as [Benign]. Clinvar id is 1183293.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANTXR1 | NM_032208.3 | c.-294G>A | 5_prime_UTR_variant | 1/18 | ENST00000303714.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANTXR1 | ENST00000303714.9 | c.-294G>A | 5_prime_UTR_variant | 1/18 | 1 | NM_032208.3 | P1 | ||
ANTXR1 | ENST00000481119.2 | n.31G>A | non_coding_transcript_exon_variant | 1/8 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0348 AC: 5061AN: 145446Hom.: 310 Cov.: 31
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GnomAD4 exome AF: 0.00486 AC: 1585AN: 325940Hom.: 72 Cov.: 0 AF XY: 0.00402 AC XY: 686AN XY: 170806
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GnomAD4 genome ? AF: 0.0349 AC: 5081AN: 145538Hom.: 312 Cov.: 31 AF XY: 0.0337 AC XY: 2369AN XY: 70314
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 20, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at