rs80356646
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The ENST00000367435.5(CDC73):c.729+44_729+51del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000104 in 1,437,930 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000093 ( 0 hom. )
Consequence
CDC73
ENST00000367435.5 intron
ENST00000367435.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.48
Genes affected
CDC73 (HGNC:16783): (cell division cycle 73) This gene encodes a tumor suppressor that is involved in transcriptional and post-transcriptional control pathways. The protein is a component of the the PAF protein complex, which associates with the RNA polymerase II subunit POLR2A and with a histone methyltransferase complex. This protein appears to facilitate the association of 3' mRNA processing factors with actively-transcribed chromatin. Mutations in this gene have been linked to hyperparathyroidism-jaw tumor syndrome, familial isolated hyperparathyroidism, and parathyroid carcinoma. [provided by RefSeq, Jul 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0000202 (3/148738) while in subpopulation AFR AF= 0.0000739 (3/40588). AF 95% confidence interval is 0.0000196. There are 0 homozygotes in gnomad4. There are 1 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAdExome4 at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDC73 | NM_024529.5 | c.729+44_729+51del | intron_variant | ENST00000367435.5 | NP_078805.3 | |||
CDC73 | XM_006711537.5 | c.729+44_729+51del | intron_variant | XP_006711600.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDC73 | ENST00000367435.5 | c.729+44_729+51del | intron_variant | 1 | NM_024529.5 | ENSP00000356405 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000202 AC: 3AN: 148738Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000931 AC: 12AN: 1289192Hom.: 0 AF XY: 0.00000617 AC XY: 4AN XY: 648194
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GnomAD4 genome AF: 0.0000202 AC: 3AN: 148738Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 1AN XY: 72446
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at