chr4-79935302-C-T

Position:

• chr4-79935302-C-T

Variant summary

Our verdict is Likely benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANTXR2	NM_058172.6	c.1429-27835G>A		intron_variant		ENST00000403729.7	NP_477520.2
ANTXR2	NM_001286780.2	c.1198-27835G>A		intron_variant			NP_001273709.1
ANTXR2	NM_001286781.2	c.1198-27835G>A		intron_variant			NP_001273710.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANTXR2	ENST00000403729.7	c.1429-27835G>A		intron_variant		1	NM_058172.6	ENSP00000385575.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 6656 AN: 147958 Hom.: 303 Cov.: 29 FAILED QC

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

Gnomad4 AFR AF: 0.00984

Gnomad4 AMR AF: 0.0630

Gnomad4 ASJ AF: 0.0252

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.0663

Gnomad4 NFE AF: 0.0392

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0428 Hom.: 39

Bravo AF: 0.0393

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.88
DANN	Benign	0.39

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: rs6823031; hg19: chr4-80856456;