chr2-222297305-T-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_181458.4(PAX3):c.86-92A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 977,376 control chromosomes in the GnomAD database, including 359,093 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.86 ( 56006 hom., cov: 35)
Exomes 𝑓: 0.86 ( 303087 hom. )
Consequence
PAX3
NM_181458.4 intron
NM_181458.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.227
Genes affected
PAX3 (HGNC:8617): (paired box 3) This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. Mutations in paired box gene 3 are associated with Waardenburg syndrome, craniofacial-deafness-hand syndrome, and alveolar rhabdomyosarcoma. The translocation t(2;13)(q35;q14), which represents a fusion between PAX3 and the forkhead gene, is a frequent finding in alveolar rhabdomyosarcoma. Alternative splicing results in transcripts encoding isoforms with different C-termini. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 2-222297305-T-G is Benign according to our data. Variant chr2-222297305-T-G is described in ClinVar as [Benign]. Clinvar id is 1288499.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX3 | NM_181458.4 | c.86-92A>C | intron_variant | ENST00000392070.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX3 | ENST00000392070.7 | c.86-92A>C | intron_variant | 1 | NM_181458.4 | A1 |
Frequencies
GnomAD3 genomes AF: 0.856 AC: 130242AN: 152176Hom.: 55955 Cov.: 35
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GnomAD4 exome AF: 0.855 AC: 705550AN: 825082Hom.: 303087 AF XY: 0.860 AC XY: 368503AN XY: 428540
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GnomAD4 genome AF: 0.856 AC: 130350AN: 152294Hom.: 56006 Cov.: 35 AF XY: 0.858 AC XY: 63926AN XY: 74470
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 24, 2018 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at