rs6823031

Variant names:

• chr4-79935302-C-T
• rs6823031
• NM_058172.6:c.1429-27835G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_058172.6(ANTXR2):​c.1429-27835G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.045 (303 hom., cov: 29)
  • Failed GnomAD Quality Control
• Consequence: ANTXR2 NM_058172.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 1 publications found

Genes affected

ANTXR2 (HGNC:21732): (ANTXR cell adhesion molecule 2) This gene encodes a receptor for anthrax toxin. The protein binds to collagen IV and laminin, suggesting that it may be involved in extracellular matrix adhesion. Mutations in this gene cause juvenile hyaline fibromatosis and infantile systemic hyalinosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

ANTXR2 Gene-Disease associations (from GenCC):

• hyaline fibromatosis syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
• juvenile hyaline fibromatosis

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, G2P
• infantile systemic hyalinosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_058172.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANTXR2	NM_058172.6	MANE Select	c.1429-27835G>A		intron	N/A	NP_477520.2
	ANTXR2	NM_001286780.2		c.1198-27835G>A		intron	N/A	NP_001273709.1
	ANTXR2	NM_001286781.2		c.1198-27835G>A		intron	N/A	NP_001273710.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANTXR2	ENST00000403729.7	TSL:1 MANE Select	c.1429-27835G>A		intron	N/A	ENSP00000385575.2
	ANTXR2	ENST00000404191.5	TSL:1	c.1198-27835G>A		intron	N/A	ENSP00000384028.1
	ANTXR2	ENST00000680913.1		c.1429-15181G>A		intron	N/A	ENSP00000505640.1

Frequencies

GnomAD3 genomes AF: 0.0450 AC: 6656 AN: 147958 Hom.: 303 Cov.: 29

Gnomad AFR AF: 0.00987

Gnomad AMI AF: 0.0211

Gnomad AMR AF: 0.0629

Gnomad ASJ AF: 0.0252

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.00658

Gnomad NFE AF: 0.0392

Gnomad OTH AF: 0.0358

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0449 AC: 6653 AN: 148066 Hom.: 303 Cov.: 29 AF XY: 0.0497 AC XY: 3582 AN XY: 72072

African (AFR) AF: 0.00984 AC: 394 AN: 40030

American (AMR) AF: 0.0630 AC: 930 AN: 14766

Ashkenazi Jewish (ASJ) AF: 0.0252 AC: 87 AN: 3454

East Asian (EAS) AF: 0.196 AC: 980 AN: 4990

South Asian (SAS) AF: 0.191 AC: 882 AN: 4614

European-Finnish (FIN) AF: 0.0663 AC: 651 AN: 9818

Middle Eastern (MID) AF: 0.0106 AC: 3 AN: 282

European-Non Finnish (NFE) AF: 0.0392 AC: 2630 AN: 67152

Other (OTH) AF: 0.0374 AC: 77 AN: 2058

Alfa AF: 0.0351 Hom.: 112

Bravo AF: 0.0393

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.88
DANN	Benign	0.39
PhyloP100		-0.93
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: rs6823031; hg19: chr4-80856456;