rs5964125
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000378588.5(CYBB):c.804+118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 698,190 control chromosomes in the GnomAD database, including 7,066 homozygotes. There are 35,503 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.17 ( 1072 hom., 5460 hem., cov: 23)
Exomes 𝑓: 0.17 ( 5994 hom. 30043 hem. )
Consequence
CYBB
ENST00000378588.5 intron
ENST00000378588.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.38
Genes affected
CYBB (HGNC:2578): (cytochrome b-245 beta chain) Cytochrome b (-245) is composed of cytochrome b alpha (CYBA) and beta (CYBB) chain. It has been proposed as a primary component of the microbicidal oxidase system of phagocytes. CYBB deficiency is one of five described biochemical defects associated with chronic granulomatous disease (CGD). In this disorder, there is decreased activity of phagocyte NADPH oxidase; neutrophils are able to phagocytize bacteria but cannot kill them in the phagocytic vacuoles. The cause of the killing defect is an inability to increase the cell's respiration and consequent failure to deliver activated oxygen into the phagocytic vacuole. [provided by RefSeq, Jul 2008]
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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=-0.8).
BP6
Variant X-37799202-A-G is Benign according to our data. Variant chrX-37799202-A-G is described in ClinVar as [Benign]. Clinvar id is 1185172.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-37799202-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYBB | NM_000397.4 | c.804+118A>G | intron_variant | ENST00000378588.5 | NP_000388.2 | |||
CYBB | XM_047441855.1 | c.498+118A>G | intron_variant | XP_047297811.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYBB | ENST00000378588.5 | c.804+118A>G | intron_variant | 1 | NM_000397.4 | ENSP00000367851 | P1 |
Frequencies
GnomAD3 genomes AF: 0.165 AC: 18431AN: 111711Hom.: 1069 Cov.: 23 AF XY: 0.160 AC XY: 5448AN XY: 33971
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GnomAD4 exome AF: 0.170 AC: 99980AN: 586426Hom.: 5994 AF XY: 0.185 AC XY: 30043AN XY: 162768
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GnomAD4 genome AF: 0.165 AC: 18443AN: 111764Hom.: 1072 Cov.: 23 AF XY: 0.160 AC XY: 5460AN XY: 34034
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Granulomatous disease, chronic, X-linked Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at