rs6659735
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001135254.2(PAX7):c.586+20832G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,656 control chromosomes in the GnomAD database, including 10,010 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 0.36 ( 10010 hom., cov: 30)
Consequence
PAX7
NM_001135254.2 intron
NM_001135254.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.445
Genes affected
PAX7 (HGNC:8621): (paired box 7) This gene is a member of the paired box (PAX) family of transcription factors. Members of this gene family typically contain a paired box domain, an octapeptide, and a paired-type homeodomain. These genes play critical roles during fetal development and cancer growth. The specific function of the paired box 7 gene is unknown but speculated to involve tumor suppression since fusion of this gene with a forkhead domain family member has been associated with alveolar rhabdomyosarcoma. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX7 | NM_001135254.2 | c.586+20832G>A | intron_variant | ENST00000420770.7 | |||
PAX7 | NM_002584.3 | c.586+20832G>A | intron_variant | ||||
PAX7 | NM_013945.3 | c.580+20832G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX7 | ENST00000420770.7 | c.586+20832G>A | intron_variant | 1 | NM_001135254.2 | P1 | |||
PAX7 | ENST00000375375.7 | c.586+20832G>A | intron_variant | 1 | |||||
PAX7 | ENST00000400661.3 | c.580+20832G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.356 AC: 53882AN: 151536Hom.: 10013 Cov.: 30
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GnomAD4 genome ? AF: 0.355 AC: 53892AN: 151656Hom.: 10010 Cov.: 30 AF XY: 0.356 AC XY: 26406AN XY: 74090
GnomAD4 genome
?
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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