chr1-193236384-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_024529.5(CDC73):c.1417+28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000137 in 1,324,950 control chromosomes in the GnomAD database, including 1 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 0.00035 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00011 ( 1 hom. )
Consequence
CDC73
NM_024529.5 intron
NM_024529.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.359
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000348 (53/152222) while in subpopulation EAS AF= 0.00443 (23/5192). AF 95% confidence interval is 0.00303. There are 0 homozygotes in gnomad4. There are 25 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 53 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000348 AC: 53AN: 152102Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000315 AC: 79AN: 251188Hom.: 1 AF XY: 0.000280 AC XY: 38AN XY: 135770
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GnomAD4 exome AF: 0.000109 AC: 128AN: 1172728Hom.: 1 Cov.: 16 AF XY: 0.000122 AC XY: 73AN XY: 597588
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GnomAD4 genome AF: 0.000348 AC: 53AN: 152222Hom.: 0 Cov.: 31 AF XY: 0.000336 AC XY: 25AN XY: 74420
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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