Genetic Variant NM_058172.6:c.866+6302A>T (chr4-80025321-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_058172.6(ANTXR2):c.866+6302A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,048 control chromosomes in the GnomAD database, including 28,626 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 0.60 ( 28626 hom., cov: 33)

Consequence

ANTXR2
NM_058172.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.842

Publications

22 publications found

Variant links:

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

ANTXR2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ANTXR2	NM_058172.6 link	c.866+6302A>T	intron_variant	Intron 10 of 16	ENST00000403729.7	NP_477520.2	P58335-4
ANTXR2	NM_001145794.2 link	c.866+6302A>T	intron_variant	Intron 10 of 15		NP_001139266.1	P58335-1
ANTXR2	NM_001286780.2 link	c.635+6302A>T	intron_variant	Intron 10 of 16		NP_001273709.1	P58335J3KPY9Q32Q26
ANTXR2	NM_001286781.2 link	c.635+6302A>T	intron_variant	Intron 10 of 16		NP_001273710.1	P58335J3KPY9A4FUA5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANTXR2	ENST00000403729.7 link	c.866+6302A>T		intron_variant	Intron 10 of 16	1	NM_058172.6	ENSP00000385575.2		P58335-4

Frequencies

GnomAD3 genomes

AF:

0.596

AC:

90536

AN:

151930

Hom.:

28606

Cov.:

show subpopulations

Gnomad AFR

AF:

0.388

Gnomad AMI

AF:

0.604

Gnomad AMR

AF:

0.730

Gnomad ASJ

AF:

0.690

Gnomad EAS

AF:

0.933

Gnomad SAS

AF:

0.772

Gnomad FIN

AF:

0.676

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.637

Gnomad OTH

AF:

0.603

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

GnomAD4 genome

AF:

0.596

AC:

90600

AN:

152048

Hom.:

28626

Cov.:

AF XY:

0.607

AC XY:

45089

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.388

AC:

16083

AN:

41476

American (AMR)

AF:

0.730

AC:

11153

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.690

AC:

2396

AN:

3472

East Asian (EAS)

AF:

0.934

AC:

4829

AN:

5172

South Asian (SAS)

AF:

0.772

AC:

3722

AN:

4822

European-Finnish (FIN)

AF:

0.676

AC:

7145

AN:

10576

Middle Eastern (MID)

AF:

0.592

AC:

174

AN:

294

European-Non Finnish (NFE)

AF:

0.637

AC:

43274

AN:

67946

Other (OTH)

AF:

0.606

AC:

1274

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1719

3437

5156

6874

8593

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

758

1516

2274

3032

3790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.612

Hom.:

3693

Bravo

AF:

0.589

Asia WGS

AF:

0.818

AC:

2823

AN:

3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

9.5

(source)

DANN

Benign

0.63

PhyloP100

-0.84

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over