10-100735764-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001304569.2(PAX2):c.25+31A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 1,027,292 control chromosomes in the GnomAD database, including 329,982 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.80 ( 49012 hom., cov: 31)
Exomes 𝑓: 0.80 ( 280970 hom. )
Consequence
PAX2
NM_001304569.2 intron
NM_001304569.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.70
Genes affected
PAX2 (HGNC:8616): (paired box 2) PAX2 encodes paired box gene 2, one of many human homologues of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcriptional supression by the tumor suppressor gene WT1. Mutations within PAX2 have been shown to result in optic nerve colobomas and renal hypoplasia. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2014]
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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=-0.88).
BP6
?
Variant 10-100735764-A-G is Benign according to our data. Variant chr10-100735764-A-G is described in ClinVar as [Benign]. Clinvar id is 1326988.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX2 | NM_001304569.2 | c.25+31A>G | intron_variant | ||||
PAX2 | NM_001374303.1 | c.25+31A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX2 | ENST00000679374.1 | c.25+31A>G | intron_variant | ||||||
PAX2 | ENST00000707078.1 | c.25+31A>G | intron_variant | ||||||
PAX2 | ENST00000553492.5 | n.131+31A>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.801 AC: 121702AN: 151862Hom.: 48964 Cov.: 31
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GnomAD4 exome AF: 0.801 AC: 700696AN: 875312Hom.: 280970 Cov.: 23 AF XY: 0.800 AC XY: 323578AN XY: 404436
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Renal coloboma syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Focal segmental glomerulosclerosis 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at