rs12393998

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003588.4(CUL4B):​c.68-5602T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.41 ( 7447 hom., 10567 hem., cov: 18)

Consequence

CUL4B
NM_003588.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CUL4BNM_003588.4 linkc.68-5602T>G intron_variant NP_003579.3 Q13620-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CUL4BENST00000680673.1 linkc.68-5602T>G intron_variant ENSP00000505084.1 Q13620-2
CUL4BENST00000681253.1 linkc.68-5602T>G intron_variant ENSP00000506259.1 Q13620-2
CUL4BENST00000681652.1 linkc.68-5602T>G intron_variant ENSP00000505176.1 Q13620-2

Frequencies

GnomAD3 genomes
AF:
0.412
AC:
42604
AN:
103450
Hom.:
7445
Cov.:
18
AF XY:
0.399
AC XY:
10532
AN XY:
26422
show subpopulations
Gnomad AFR
AF:
0.633
Gnomad AMI
AF:
0.274
Gnomad AMR
AF:
0.444
Gnomad ASJ
AF:
0.366
Gnomad EAS
AF:
0.337
Gnomad SAS
AF:
0.295
Gnomad FIN
AF:
0.284
Gnomad MID
AF:
0.376
Gnomad NFE
AF:
0.309
Gnomad OTH
AF:
0.406
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.412
AC:
42640
AN:
103477
Hom.:
7447
Cov.:
18
AF XY:
0.399
AC XY:
10567
AN XY:
26459
show subpopulations
Gnomad4 AFR
AF:
0.633
Gnomad4 AMR
AF:
0.444
Gnomad4 ASJ
AF:
0.366
Gnomad4 EAS
AF:
0.337
Gnomad4 SAS
AF:
0.293
Gnomad4 FIN
AF:
0.284
Gnomad4 NFE
AF:
0.309
Gnomad4 OTH
AF:
0.408
Alfa
AF:
0.332
Hom.:
28848
Bravo
AF:
0.439

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.13
DANN
Benign
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12393998; hg19: chrX-119700082; API