chrX-120526946-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001079872.2(CUL4B):c.2593-90G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 464,073 control chromosomes in the GnomAD database, including 690 homozygotes. There are 2,489 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.058 ( 491 hom., 1796 hem., cov: 23)
Exomes 𝑓: 0.0090 ( 199 hom. 693 hem. )
Consequence
CUL4B
NM_001079872.2 intron
NM_001079872.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.372
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
Variant X-120526946-C-T is Benign according to our data. Variant chrX-120526946-C-T is described in ClinVar as [Benign]. Clinvar id is 1222218.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUL4B | NM_001079872.2 | c.2593-90G>A | intron_variant | ENST00000371322.11 | |||
CUL4B | NM_001330624.2 | c.2608-90G>A | intron_variant | ||||
CUL4B | NM_001369145.1 | c.2059-90G>A | intron_variant | ||||
CUL4B | NM_003588.4 | c.2647-90G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUL4B | ENST00000371322.11 | c.2593-90G>A | intron_variant | 1 | NM_001079872.2 |
Frequencies
GnomAD3 genomes AF: 0.0578 AC: 6478AN: 112091Hom.: 488 Cov.: 23 AF XY: 0.0517 AC XY: 1775AN XY: 34347
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GnomAD4 exome AF: 0.00904 AC: 3181AN: 351930Hom.: 199 AF XY: 0.00759 AC XY: 693AN XY: 91246
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GnomAD4 genome AF: 0.0580 AC: 6507AN: 112143Hom.: 491 Cov.: 23 AF XY: 0.0522 AC XY: 1796AN XY: 34409
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 10, 2019 | - - |
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