4-80005847-C-T

Variant summary

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

The NM_058172.6(ANTXR2):c.1041+2674G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,932 control chromosomes in the GnomAD database, including 20,095 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 0.48 (20095 hom., cov: 31)
• Consequence: ANTXR2 NM_058172.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANTXR2	NM_058172.6	c.1041+2674G>A		intron_variant		ENST00000403729.7
ANTXR2	NM_001145794.2	c.1041+2674G>A		intron_variant
ANTXR2	NM_001286780.2	c.810+2674G>A		intron_variant
ANTXR2	NM_001286781.2	c.810+2674G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANTXR2	ENST00000403729.7	c.1041+2674G>A		intron_variant		1	NM_058172.6	P1

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72989 AN: 151812 Hom.: 20081 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.481 AC: 73031 AN: 151932 Hom.: 20095 Cov.: 31 AF XY: 0.496 AC XY: 36823 AN XY: 74266

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.472

Alfa AF: 0.527 Hom.: 43874

Bravo AF: 0.467

Asia WGS AF: 0.755 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.3
Dann	Benign	0.37

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: rs12504282; hg19: chr4-80927001;