Variant rs3794624 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.58+290C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 594,852 control chromosomes in the GnomAD database, including 28,096 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6556 hom., cov: 34)

Exomes 𝑓: 0.30 ( 21540 hom. )

Consequence

CYBA
NM_000101.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.95

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=-0.65).

BP6

Variant 16-88650666-G-A is Benign according to our data. Variant chr16-88650666-G-A is described in ClinVar as [Benign]. Clinvar id is 1229308.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYBA	NM_000101.4 linkuse as main transcript	c.58+290C>T		intron_variant		ENST00000261623.8	NP_000092.2
CYBA	XM_011522905.4 linkuse as main transcript	c.58+290C>T		intron_variant			XP_011521207.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYBA	ENST00000261623.8 linkuse as main transcript	c.58+290C>T		intron_variant		1	NM_000101.4	ENSP00000261623	P1

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43295

AN:

152104

Hom.:

6556

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.542

Gnomad AMR

AF:

0.280

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.352

Gnomad OTH

AF:

0.256

GnomAD3 exomes

AF:

0.259

AC:

22241

AN:

85832

Hom.:

3308

AF XY:

0.254

AC XY:

11978

AN XY:

47176

show subpopulations

Gnomad AFR exome

AF:

0.193

Gnomad AMR exome

AF:

0.261

Gnomad ASJ exome

AF:

0.246

Gnomad EAS exome

AF:

0.148

Gnomad SAS exome

AF:

0.127

Gnomad FIN exome

AF:

0.353

Gnomad NFE exome

AF:

0.350

Gnomad OTH exome

AF:

0.278

GnomAD4 exome

AF:

0.296

AC:

131229

AN:

442630

Hom.:

21540

Cov.:

AF XY:

0.285

AC XY:

67719

AN XY:

237846

show subpopulations

Gnomad4 AFR exome

AF:

0.192

Gnomad4 AMR exome

AF:

0.259

Gnomad4 ASJ exome

AF:

0.251

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.129

Gnomad4 FIN exome

AF:

0.362

Gnomad4 NFE exome

AF:

0.351

Gnomad4 OTH exome

AF:

0.287

GnomAD4 genome

AF:

0.284

AC:

43301

AN:

152222

Hom.:

6556

Cov.:

AF XY:

0.280

AC XY:

20819

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.194

Gnomad4 AMR

AF:

0.280

Gnomad4 ASJ

AF:

0.247

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.127

Gnomad4 FIN

AF:

0.343

Gnomad4 NFE

AF:

0.352

Gnomad4 OTH

AF:

0.254

Alfa

AF:

0.326

Hom.:

11404

Bravo

AF:

0.278

Asia WGS

AF:

0.142

AC:

495

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 08, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

6.1

DANN

Benign

0.95

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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