rs6749826

Variant names:

• chr2-69181897-C-A
• rs6749826
• NM_032208.3:c.1185+16C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-69181897-C-A
• chr2-69181897-C-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.1185+16C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 1,611,934 control chromosomes in the GnomAD database, including 174,406 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.47 (17232 hom., cov: 31)
  • Exomes 𝑓: 0.46 (157174 hom.)
• Consequence: ANTXR1 NM_032208.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:6
• Conservation: PhyloP100: -0.406

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]

RNA5SP96 (HGNC:42894): (RNA, 5S ribosomal pseudogene 96)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 2-69181897-C-A is Benign according to our data. Variant chr2-69181897-C-A is described in ClinVar as [Benign]. Clinvar id is 262019.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-69181897-C-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANTXR1	NM_032208.3	c.1185+16C>A		intron_variant	Intron 15 of 17	ENST00000303714.9	NP_115584.1
RNA5SP96		n.69181897C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANTXR1	ENST00000303714.9	c.1185+16C>A		intron_variant	Intron 15 of 17	1	NM_032208.3	ENSP00000301945.4
RNA5SP96	ENST00000516041.1	n.107G>T		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70909 AN: 151766 Hom.: 17228 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.484

GnomAD2 exomes AF: 0.481 AC: 120775 AN: 251062 AF XY: 0.487

Gnomad AFR exome AF: 0.511

Gnomad AMR exome AF: 0.477

Gnomad ASJ exome AF: 0.419

Gnomad EAS exome AF: 0.762

Gnomad FIN exome AF: 0.302

Gnomad NFE exome AF: 0.424

Gnomad OTH exome AF: 0.472

GnomAD4 exome AF: 0.456 AC: 665263 AN: 1460048 Hom.: 157174 Cov.: 32 AF XY: 0.461 AC XY: 335229 AN XY: 726450

Gnomad4 AFR exome AF: 0.518 AC: 17337 AN: 33442

Gnomad4 AMR exome AF: 0.473 AC: 21157 AN: 44704

Gnomad4 ASJ exome AF: 0.423 AC: 11039 AN: 26116

Gnomad4 EAS exome AF: 0.781 AC: 30988 AN: 39688

Gnomad4 SAS exome AF: 0.658 AC: 56701 AN: 86186

Gnomad4 FIN exome AF: 0.302 AC: 16092 AN: 53370

Gnomad4 NFE exome AF: 0.432 AC: 479878 AN: 1110460

Gnomad4 Remaining exome AF: 0.478 AC: 28851 AN: 60320

GnomAD4 genome AF: 0.467 AC: 70950 AN: 151886 Hom.: 17232 Cov.: 31 AF XY: 0.467 AC XY: 34695 AN XY: 74220

Gnomad4 AFR AF: 0.508 AC: 0.508241 AN: 0.508241

Gnomad4 AMR AF: 0.487 AC: 0.486692 AN: 0.486692

Gnomad4 ASJ AF: 0.422 AC: 0.422344 AN: 0.422344

Gnomad4 EAS AF: 0.767 AC: 0.767352 AN: 0.767352

Gnomad4 SAS AF: 0.672 AC: 0.672292 AN: 0.672292

Gnomad4 FIN AF: 0.296 AC: 0.296219 AN: 0.296219

Gnomad4 NFE AF: 0.429 AC: 0.429335 AN: 0.429335

Gnomad4 OTH AF: 0.480 AC: 0.479563 AN: 0.479563

Alfa AF: 0.452 Hom.: 4610

Bravo AF: 0.481

Asia WGS AF: 0.647 AC: 2251 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 10, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Benign:1

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Capillary infantile hemangioma Benign:1

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

GAPO syndrome Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.44
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

Publications

LitVar

Other links and lift over

dbSNP: rs6749826; hg19: chr2-69409029;