4-80072642-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_058172.6(ANTXR2):c.-82C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 1,359,096 control chromosomes in the GnomAD database, including 102,550 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.38 ( 11501 hom., cov: 31)
Exomes 𝑓: 0.38 ( 91049 hom. )
Consequence
ANTXR2
NM_058172.6 5_prime_UTR
NM_058172.6 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.333
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 4-80072642-G-T is Benign according to our data. Variant chr4-80072642-G-T is described in ClinVar as [Benign]. Clinvar id is 349890.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANTXR2 | NM_058172.6 | c.-82C>A | 5_prime_UTR_variant | 1/17 | ENST00000403729.7 | ||
ANTXR2 | NM_001145794.2 | c.-82C>A | 5_prime_UTR_variant | 1/16 | |||
ANTXR2 | NM_001286780.2 | c.-80+753C>A | intron_variant | ||||
ANTXR2 | NM_001286781.2 | c.-80+67C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANTXR2 | ENST00000403729.7 | c.-82C>A | 5_prime_UTR_variant | 1/17 | 1 | NM_058172.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.385 AC: 58356AN: 151652Hom.: 11489 Cov.: 31
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GnomAD4 exome AF: 0.384 AC: 463464AN: 1207324Hom.: 91049 Cov.: 33 AF XY: 0.389 AC XY: 226153AN XY: 581580
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hyaline fibromatosis syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at