Variant rs4782308 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000101.4(CYBA):c.203+36C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 1,580,492 control chromosomes in the GnomAD database, including 353,172 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.64 ( 31958 hom., cov: 33)

Exomes 𝑓: 0.67 ( 321214 hom. )

Consequence

CYBA
NM_000101.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.00300

Variant links:

Genes affected

CYBA (HGNC:2577): (cytochrome b-245 alpha chain) Cytochrome b is comprised of a light chain (alpha) and a heavy chain (beta). This gene encodes the light, alpha subunit which has been proposed as a primary component of the microbicidal oxidase system of phagocytes. Mutations in this gene are associated with autosomal recessive chronic granulomatous disease (CGD), that is characterized by the failure of activated phagocytes to generate superoxide, which is important for the microbicidal activity of these cells. [provided by RefSeq, Jul 2008]

CYBA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 16-88647065-G-A is Benign according to our data. Variant chr16-88647065-G-A is described in ClinVar as [Benign]. Clinvar id is 1172931.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYBA	NM_000101.4 link	c.203+36C>T		intron_variant		ENST00000261623.8	NP_000092.2	P13498B4DT46
CYBA	XM_011522905.4 link	c.203+36C>T		intron_variant			XP_011521207.1	H3BNP7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYBA	ENST00000261623.8 link	c.203+36C>T		intron_variant		1	NM_000101.4	ENSP00000261623.3		P13498

Frequencies

GnomAD3 genomes

AF:

0.642

AC:

97613

AN:

151952

Hom.:

31936

Cov.:

show subpopulations

Gnomad AFR

AF:

0.522

Gnomad AMI

AF:

0.689

Gnomad AMR

AF:

0.717

Gnomad ASJ

AF:

0.567

Gnomad EAS

AF:

0.862

Gnomad SAS

AF:

0.620

Gnomad FIN

AF:

0.819

Gnomad MID

AF:

0.547

Gnomad NFE

AF:

0.660

Gnomad OTH

AF:

0.625

GnomAD3 exomes

AF:

0.680

AC:

152263

AN:

223910

Hom.:

52765

AF XY:

0.672

AC XY:

82228

AN XY:

122302

show subpopulations

Gnomad AFR exome

AF:

0.523

Gnomad AMR exome

AF:

0.764

Gnomad ASJ exome

AF:

0.554

Gnomad EAS exome

AF:

0.856

Gnomad SAS exome

AF:

0.613

Gnomad FIN exome

AF:

0.812

Gnomad NFE exome

AF:

0.657

Gnomad OTH exome

AF:

0.648

GnomAD4 exome

AF:

0.668

AC:

953492

AN:

1428422

Hom.:

321214

Cov.:

AF XY:

0.666

AC XY:

473340

AN XY:

711196

show subpopulations

Gnomad4 AFR exome

AF:

0.520

Gnomad4 AMR exome

AF:

0.753

Gnomad4 ASJ exome

AF:

0.570

Gnomad4 EAS exome

AF:

0.862

Gnomad4 SAS exome

AF:

0.616

Gnomad4 FIN exome

AF:

0.806

Gnomad4 NFE exome

AF:

0.663

Gnomad4 OTH exome

AF:

0.657

GnomAD4 genome

AF:

0.642

AC:

97674

AN:

152070

Hom.:

31958

Cov.:

AF XY:

0.651

AC XY:

48376

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.521

Gnomad4 AMR

AF:

0.717

Gnomad4 ASJ

AF:

0.567

Gnomad4 EAS

AF:

0.863

Gnomad4 SAS

AF:

0.621

Gnomad4 FIN

AF:

0.819

Gnomad4 NFE

AF:

0.660

Gnomad4 OTH

AF:

0.626

Alfa

AF:

0.633

Hom.:

5525

Bravo

AF:

0.632

Asia WGS

AF:

0.713

AC:

2480

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 91% of patients studied by a panel of primary immunodeficiencies. Number of patients: 86. Only high quality variants are reported. -

Granulomatous disease, chronic, autosomal recessive, cytochrome b-negative

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jun 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.2

DANN

Benign

0.84

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

2.3

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over