chrX-120527062-C-CT

Variant names:

• chrX-120527062-C-CT
• rs918835696
• NM_001079872.2:c.2593-207dupA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_001079872.2(CUL4B):​c.2593-207dupA 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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.17
• Publications: 0 publications found

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]

CUL4B Gene-Disease associations (from GenCC):

• X-linked intellectual disability, Cabezas type

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet, G2P

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 21. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 40 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CUL4B	NM_001079872.2	c.2593-207dupA		intron_variant	Intron 19 of 19	ENST00000371322.11	NP_001073341.1
CUL4B	NM_003588.4	c.2647-207dupA		intron_variant	Intron 21 of 21		NP_003579.3
CUL4B	NM_001330624.2	c.2608-207dupA		intron_variant	Intron 20 of 20		NP_001317553.1
CUL4B	NM_001369145.1	c.2059-207dupA		intron_variant	Intron 19 of 19		NP_001356074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CUL4B	ENST00000371322.11	c.2593-207_2593-206insA		intron_variant	Intron 19 of 19	1	NM_001079872.2	ENSP00000360373.5
CUL4B	ENST00000681206.1	c.2707-207_2707-206insA		intron_variant	Intron 22 of 22			ENSP00000505480.1
CUL4B	ENST00000680673.1	c.2647-207_2647-206insA		intron_variant	Intron 21 of 21			ENSP00000505084.1
CUL4B	ENST00000681253.1	c.2647-207_2647-206insA		intron_variant	Intron 22 of 22			ENSP00000506259.1
CUL4B	ENST00000681652.1	c.2647-207_2647-206insA		intron_variant	Intron 24 of 24			ENSP00000505176.1
CUL4B	ENST00000336592.11	c.2608-207_2608-206insA		intron_variant	Intron 20 of 20	5		ENSP00000338919.6
CUL4B	ENST00000674137.11	c.2599-207_2599-206insA		intron_variant	Intron 19 of 19			ENSP00000501019.6
CUL4B	ENST00000681090.1	c.2500-207_2500-206insA		intron_variant	Intron 19 of 19			ENSP00000506288.1
CUL4B	ENST00000404115.8	c.2440-207_2440-206insA		intron_variant	Intron 18 of 18	1		ENSP00000384109.4
CUL4B	ENST00000679927.1	c.2248-207_2248-206insA		intron_variant	Intron 20 of 20			ENSP00000505603.1
CUL4B	ENST00000371323.3	c.2059-207_2059-206insA		intron_variant	Intron 19 of 19	5		ENSP00000360374.3
CUL4B	ENST00000680474.1	c.*39-207_*39-206insA		intron_variant	Intron 19 of 19			ENSP00000505562.1
CUL4B	ENST00000679844.1	c.1930-207_1930-206insA		intron_variant	Intron 17 of 17			ENSP00000505239.1
CUL4B	ENST00000673919.1	n.*2040-207_*2040-206insA		intron_variant	Intron 20 of 20			ENSP00000500994.1
CUL4B	ENST00000674073.2	n.*149-207_*149-206insA		intron_variant	Intron 17 of 17			ENSP00000501262.2
CUL4B	ENST00000679405.1	n.*1802-207_*1802-206insA		intron_variant	Intron 21 of 21			ENSP00000504985.1
CUL4B	ENST00000679432.1	n.*1802-207_*1802-206insA		intron_variant	Intron 21 of 21			ENSP00000505343.1
CUL4B	ENST00000680918.1	n.*1509-207_*1509-206insA		intron_variant	Intron 17 of 17			ENSP00000505955.1
CUL4B	ENST00000681080.1	n.*1802-207_*1802-206insA		intron_variant	Intron 19 of 19			ENSP00000505898.1
CUL4B	ENST00000681189.1	n.*759-207_*759-206insA		intron_variant	Intron 19 of 19			ENSP00000505973.1
CUL4B	ENST00000681333.1	n.*3486-207_*3486-206insA		intron_variant	Intron 16 of 16			ENSP00000505739.1
CUL4B	ENST00000681908.1	n.*765-207_*765-206insA		intron_variant	Intron 19 of 19			ENSP00000505777.1

Frequencies

GnomAD3 genomes AF: 0.0227 AC: 2285 AN: 100793 Hom.: 40 Cov.: 21

Gnomad AFR AF: 0.00619

Gnomad AMI AF: 0.0111

Gnomad AMR AF: 0.0144

Gnomad ASJ AF: 0.0217

Gnomad EAS AF: 0.00939

Gnomad SAS AF: 0.0144

Gnomad FIN AF: 0.0283

Gnomad MID AF: 0.0425

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0227 AC: 2285 AN: 100788 Hom.: 40 Cov.: 21 AF XY: 0.0169 AC XY: 468 AN XY: 27682

African (AFR) AF: 0.00618 AC: 174 AN: 28147

American (AMR) AF: 0.0145 AC: 135 AN: 9339

Ashkenazi Jewish (ASJ) AF: 0.0217 AC: 53 AN: 2443

East Asian (EAS) AF: 0.00943 AC: 31 AN: 3289

South Asian (SAS) AF: 0.0145 AC: 34 AN: 2341

European-Finnish (FIN) AF: 0.0283 AC: 116 AN: 4092

Middle Eastern (MID) AF: 0.0412 AC: 8 AN: 194

European-Non Finnish (NFE) AF: 0.0348 AC: 1705 AN: 48980

Other (OTH) AF: 0.0165 AC: 22 AN: 1331

Alfa AF: 0.00528 Hom.: 22

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Sep 02, 2019

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs918835696; hg19: chrX-119660917;