chr2-222201034-T-TAC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_181458.4(PAX3):c.*373_*374insGT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 793,502 control chromosomes in the GnomAD database, including 581 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.051 ( 553 hom., cov: 31)
Exomes 𝑓: 0.0095 ( 28 hom. )
Consequence
PAX3
NM_181458.4 3_prime_UTR
NM_181458.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.01
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 2-222201034-T-TAC is Benign according to our data. Variant chr2-222201034-T-TAC is described in ClinVar as [Benign]. Clinvar id is 1291395.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX3 | NM_181458.4 | c.*373_*374insGT | 3_prime_UTR_variant | 9/9 | ENST00000392070.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX3 | ENST00000392070.7 | c.*373_*374insGT | 3_prime_UTR_variant | 9/9 | 1 | NM_181458.4 | A1 | ||
PAX3 | ENST00000392069.6 | c.*139_*140insGT | 3_prime_UTR_variant | 10/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0512 AC: 7641AN: 149178Hom.: 554 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
7641
AN:
149178
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00946 AC: 6096AN: 644230Hom.: 28 Cov.: 2 AF XY: 0.00842 AC XY: 2805AN XY: 333214
GnomAD4 exome
AF:
AC:
6096
AN:
644230
Hom.:
Cov.:
2
AF XY:
AC XY:
2805
AN XY:
333214
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0513 AC: 7658AN: 149272Hom.: 553 Cov.: 31 AF XY: 0.0491 AC XY: 3573AN XY: 72778
GnomAD4 genome
?
AF:
AC:
7658
AN:
149272
Hom.:
Cov.:
31
AF XY:
AC XY:
3573
AN XY:
72778
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
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 | Aug 13, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at