chrX-120527062-C-CT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001079872.2(CUL4B):c.2593-207_2593-206insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0227 in 100,788 control chromosomes in the GnomAD database, including 40 homozygotes. There are 468 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.023 ( 40 hom., 468 hem., cov: 21)
Consequence
CUL4B
NM_001079872.2 intron
NM_001079872.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.17
Genes affected
CUL4B (HGNC:2555): (cullin 4B) This gene is a member of the cullin family. The encoded protein forms a complex that functions as an E3 ubiquitin ligase and catalyzes the polyubiquitination of specific protein substrates in the cell. The protein interacts with a ring finger protein, and is required for the proteolysis of several regulators of DNA replication including chromatin licensing and DNA replication factor 1 and cyclin E. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant X-120527062-C-CT is Benign according to our data. Variant chrX-120527062-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 1213151.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0227 (2285/100788) while in subpopulation NFE AF= 0.0348 (1705/48980). AF 95% confidence interval is 0.0334. There are 40 homozygotes in gnomad4. There are 468 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 40 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUL4B | NM_001079872.2 | c.2593-207_2593-206insA | intron_variant | ENST00000371322.11 | |||
CUL4B | NM_001330624.2 | c.2608-207_2608-206insA | intron_variant | ||||
CUL4B | NM_001369145.1 | c.2059-207_2059-206insA | intron_variant | ||||
CUL4B | NM_003588.4 | c.2647-207_2647-206insA | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUL4B | ENST00000371322.11 | c.2593-207_2593-206insA | intron_variant | 1 | NM_001079872.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0227 AC: 2285AN: 100793Hom.: 40 Cov.: 21 AF XY: 0.0169 AC XY: 468AN XY: 27679
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0227 AC: 2285AN: 100788Hom.: 40 Cov.: 21 AF XY: 0.0169 AC XY: 468AN XY: 27682
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 02, 2019 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at