rs769582983
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000278.5(PAX2):c.213-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,612,246 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
PAX2
NM_000278.5 intron
NM_000278.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.783
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 -16 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 10-100750674-C-T is Benign according to our data. Variant chr10-100750674-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 259213.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX2 | NM_000278.5 | c.213-20C>T | intron_variant | ENST00000355243.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX2 | ENST00000355243.8 | c.213-20C>T | intron_variant | 1 | NM_000278.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000402 AC: 10AN: 248900Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 134990
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GnomAD4 exome AF: 0.000108 AC: 158AN: 1459996Hom.: 0 Cov.: 32 AF XY: 0.0000950 AC XY: 69AN XY: 726374
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GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74378
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Renal coloboma syndrome;C4014925:Focal segmental glomerulosclerosis 7 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at