16-88643389-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000101.4(CYBA):c.552G>A(p.Gln184Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000724 in 1,381,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Consequence
CYBA
NM_000101.4 synonymous
NM_000101.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.305
Publications
0 publications found
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 Gene-Disease associations (from GenCC):
- granulomatous disease, chronic, autosomal recessive, cytochrome b-negativeInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- chronic granulomatous diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
Variant 16-88643389-C-T is Benign according to our data. Variant chr16-88643389-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2753354.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.305 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 7.24e-7 AC: 1AN: 1381662Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 681614 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1381662
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
681614
show subpopulations
African (AFR)
AF:
AC:
0
AN:
29680
American (AMR)
AF:
AC:
0
AN:
34876
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24720
East Asian (EAS)
AF:
AC:
0
AN:
34590
South Asian (SAS)
AF:
AC:
0
AN:
78280
European-Finnish (FIN)
AF:
AC:
0
AN:
42476
Middle Eastern (MID)
AF:
AC:
0
AN:
4952
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1074748
Other (OTH)
AF:
AC:
0
AN:
57340
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Granulomatous disease, chronic, autosomal recessive, cytochrome b-negative Benign:1
Mar 01, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.