X-120529942-G-GT

Position:

• chrX-120529942-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001079872.2(CUL4B):​c.2592+159dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.53 (11815 hom., 14733 hem., cov: 0)
• Consequence: CUL4B NM_001079872.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.328

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-120529942-G-GT is Benign according to our data. Variant chrX-120529942-G-GT is described in ClinVar as [Benign]. Clinvar id is 1231177.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CUL4B	NM_001079872.2	c.2592+159dupA		intron_variant		ENST00000371322.11	NP_001073341.1
CUL4B	NM_003588.4	c.2646+159dupA		intron_variant			NP_003579.3
CUL4B	NM_001330624.2	c.2607+159dupA		intron_variant			NP_001317553.1
CUL4B	NM_001369145.1	c.2058+159dupA		intron_variant			NP_001356074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CUL4B	ENST00000371322.11	c.2592+159_2592+160insA		intron_variant		1	NM_001079872.2	ENSP00000360373.5
CUL4B	ENST00000681206.1	c.2706+159_2706+160insA		intron_variant				ENSP00000505480.1
CUL4B	ENST00000680673.1	c.2646+159_2646+160insA		intron_variant				ENSP00000505084.1
CUL4B	ENST00000681253.1	c.2646+159_2646+160insA		intron_variant				ENSP00000506259.1
CUL4B	ENST00000681652.1	c.2646+159_2646+160insA		intron_variant				ENSP00000505176.1
CUL4B	ENST00000336592.11	c.2607+159_2607+160insA		intron_variant		5		ENSP00000338919.6
CUL4B	ENST00000674137.11	c.2598+159_2598+160insA		intron_variant				ENSP00000501019.6
CUL4B	ENST00000681090.1	c.2499+159_2499+160insA		intron_variant				ENSP00000506288.1
CUL4B	ENST00000404115.8	c.2439+2479_2439+2480insA		intron_variant		1		ENSP00000384109.4
CUL4B	ENST00000679927.1	c.2247+159_2247+160insA		intron_variant				ENSP00000505603.1
CUL4B	ENST00000371323.3	c.2058+159_2058+160insA		intron_variant		5		ENSP00000360374.3
CUL4B	ENST00000680474.1	c.2034+159_2034+160insA		intron_variant				ENSP00000505562.1
CUL4B	ENST00000679844.1	c.1929+159_1929+160insA		intron_variant				ENSP00000505239.1
CUL4B	ENST00000673919.1	n.*2039+159_*2039+160insA		intron_variant				ENSP00000500994.1
CUL4B	ENST00000674073.2	n.*148+159_*148+160insA		intron_variant				ENSP00000501262.2
CUL4B	ENST00000679405.1	n.*1801+159_*1801+160insA		intron_variant				ENSP00000504985.1
CUL4B	ENST00000679432.1	n.*1801+159_*1801+160insA		intron_variant				ENSP00000505343.1
CUL4B	ENST00000680918.1	n.*1508+159_*1508+160insA		intron_variant				ENSP00000505955.1
CUL4B	ENST00000681080.1	n.*1801+159_*1801+160insA		intron_variant				ENSP00000505898.1
CUL4B	ENST00000681189.1	n.*758+159_*758+160insA		intron_variant				ENSP00000505973.1
CUL4B	ENST00000681333.1	n.*3485+159_*3485+160insA		intron_variant				ENSP00000505739.1
CUL4B	ENST00000681908.1	n.*764+159_*764+160insA		intron_variant				ENSP00000505777.1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 55382 AN: 104559 Hom.: 11822 Cov.: 0 AF XY: 0.524 AC XY: 14732 AN XY: 28123

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.552

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.529 AC: 55365 AN: 104569 Hom.: 11815 Cov.: 0 AF XY: 0.523 AC XY: 14733 AN XY: 28145

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.552

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 18, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs76254851; hg19: chrX-119663797;