Variant rs6749826 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.406

Variant links:

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 links:

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

RNA5SP96 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ANTXR1	NM_032208.3 linkuse as main transcript	c.1185+16C>A		intron_variant		ENST00000303714.9	NP_115584.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANTXR1	ENST00000303714.9 linkuse as main transcript	c.1185+16C>A		intron_variant		1	NM_032208.3	ENSP00000301945	P1	Q9H6X2-1
RNA5SP96	ENST00000516041.1 linkuse as main transcript	n.107G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.467

AC:

70909

AN:

151766

Hom.:

17228

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.481

AC:

120775

AN:

251062

Hom.:

30946

AF XY:

0.487

AC XY:

66096

AN XY:

135714

show subpopulations

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 SAS exome

AF:

0.660

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.:

AF XY:

0.461

AC XY:

335229

AN XY:

726450

show subpopulations

Gnomad4 AFR exome

AF:

0.518

Gnomad4 AMR exome

AF:

0.473

Gnomad4 ASJ exome

AF:

0.423

Gnomad4 EAS exome

AF:

0.781

Gnomad4 SAS exome

AF:

0.658

Gnomad4 FIN exome

AF:

0.302

Gnomad4 NFE exome

AF:

0.432

Gnomad4 OTH exome

AF:

0.478

GnomAD4 genome

AF:

0.467

AC:

70950

AN:

151886

Hom.:

17232

Cov.:

AF XY:

0.467

AC XY:

34695

AN XY:

74220

show subpopulations

Gnomad4 AFR

AF:

0.508

Gnomad4 AMR

AF:

0.487

Gnomad4 ASJ

AF:

0.422

Gnomad4 EAS

AF:

0.767

Gnomad4 SAS

AF:

0.672

Gnomad4 FIN

AF:

0.296

Gnomad4 NFE

AF:

0.429

Gnomad4 OTH

AF:

0.480

Alfa

AF:

0.451

Hom.:

4503

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

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Capillary infantile hemangioma

Benign:1

Benign, criteria provided, single submitter

clinical testing

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Jul 07, 2023

- -

GAPO syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.1

DANN

Benign

0.44

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over