rs79337921

Variant names:

• chr2-69152148-G-A
• rs79337921
• NM_032208.3:c.952-21G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-69152148-G-A
• chr2-69152148-G-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_032208.3(ANTXR1):​c.952-21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00827 in 1,611,682 control chromosomes in the GnomAD database, including 272 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0092 (29 hom., cov: 32)
  • Exomes 𝑓: 0.0082 (243 hom.)
• Consequence: ANTXR1 NM_032208.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.84
• 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: G2P, Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics
• capillary infantile hemangioma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000300924 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 2-69152148-G-A is Benign according to our data. Variant chr2-69152148-G-A is described in ClinVar as Benign. ClinVar VariationId is 1259793.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0882 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032208.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANTXR1	NM_032208.3	MANE Select	c.952-21G>A		intron	N/A	NP_115584.1	Q9H6X2-1
	ANTXR1	NM_053034.2		c.952-21G>A		intron	N/A	NP_444262.1	Q9H6X2-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANTXR1	ENST00000303714.9	TSL:1 MANE Select	c.952-21G>A		intron	N/A	ENSP00000301945.4	Q9H6X2-1
	ANTXR1	ENST00000409349.7	TSL:1	c.952-21G>A		intron	N/A	ENSP00000386494.3	Q9H6X2-2
	ANTXR1	ENST00000894109.1		c.952-18100G>A		intron	N/A	ENSP00000564168.1

Frequencies

GnomAD3 genomes AF: 0.00919 AC: 1397 AN: 152074 Hom.: 29 Cov.: 32

Gnomad AFR AF: 0.00174

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0175

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.00476

Gnomad FIN AF: 0.0110

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00525

Gnomad OTH AF: 0.00766

GnomAD2 exomes AF: 0.0142 AC: 3558 AN: 251168 AF XY: 0.0126

Gnomad AFR exome AF: 0.00178

Gnomad AMR exome AF: 0.0206

Gnomad ASJ exome AF: 0.000595

Gnomad EAS exome AF: 0.0969

Gnomad FIN exome AF: 0.0110

Gnomad NFE exome AF: 0.00575

Gnomad OTH exome AF: 0.0106

GnomAD4 exome AF: 0.00818 AC: 11940 AN: 1459490 Hom.: 243 Cov.: 30 AF XY: 0.00791 AC XY: 5742 AN XY: 726214

African (AFR) AF: 0.00126 AC: 42 AN: 33438

American (AMR) AF: 0.0212 AC: 950 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.000459 AC: 12 AN: 26124

East Asian (EAS) AF: 0.105 AC: 4163 AN: 39670

South Asian (SAS) AF: 0.00240 AC: 207 AN: 86220

European-Finnish (FIN) AF: 0.0112 AC: 591 AN: 52988

Middle Eastern (MID) AF: 0.00191 AC: 11 AN: 5764

European-Non Finnish (NFE) AF: 0.00494 AC: 5489 AN: 1110238

Other (OTH) AF: 0.00787 AC: 475 AN: 60330

GnomAD4 genome AF: 0.00916 AC: 1394 AN: 152192 Hom.: 29 Cov.: 32 AF XY: 0.00969 AC XY: 721 AN XY: 74402

African (AFR) AF: 0.00173 AC: 72 AN: 41516

American (AMR) AF: 0.0174 AC: 266 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3470

East Asian (EAS) AF: 0.0952 AC: 491 AN: 5160

South Asian (SAS) AF: 0.00455 AC: 22 AN: 4832

European-Finnish (FIN) AF: 0.0110 AC: 117 AN: 10606

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00524 AC: 356 AN: 68000

Other (OTH) AF: 0.00758 AC: 16 AN: 2110

Alfa AF: 0.00491 Hom.: 2

Bravo AF: 0.0105

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.013
DANN	Benign	0.82
PhyloP100		-2.8
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: rs79337921; hg19: chr2-69379280;