chr4-79929167-T-C

Position:

• chr4-79929167-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_058172.6(ANTXR2):​c.1429-21700A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,156 control chromosomes in the GnomAD database, including 2,475 homozygotes. 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 0.12 (2475 hom., cov: 32)
• Consequence: ANTXR2 NM_058172.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANTXR2	NM_058172.6	c.1429-21700A>G		intron_variant		ENST00000403729.7	NP_477520.2
ANTXR2	NM_001286780.2	c.1198-21700A>G		intron_variant			NP_001273709.1
ANTXR2	NM_001286781.2	c.1198-21700A>G		intron_variant			NP_001273710.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANTXR2	ENST00000403729.7	c.1429-21700A>G		intron_variant		1	NM_058172.6	ENSP00000385575	P1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18271 AN: 152038 Hom.: 2469 Cov.: 32

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.120 AC: 18288 AN: 152156 Hom.: 2475 Cov.: 32 AF XY: 0.134 AC XY: 9992 AN XY: 74366

Gnomad4 AFR AF: 0.0690

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.0688

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0716 Hom.: 201

Bravo AF: 0.126

Asia WGS AF: 0.458 AC: 1588 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.72

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: rs4690127; hg19: chr4-80850321;