rs1625859
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000423083.1(NCF1B):n.158+1449A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00015 ( 0 hom., cov: 14)
Consequence
NCF1B
ENST00000423083.1 intron
ENST00000423083.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.24
Publications
1 publications found
Genes affected
NCF1B (HGNC:32522): (neutrophil cytosolic factor 1B (pseudogene)) Predicted to enable superoxide-generating NADPH oxidase activator activity. Predicted to be involved in respiratory burst and superoxide anion generation. Predicted to be part of NADPH oxidase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| NCF1B | NR_003186.1 | n.158+1449A>G | intron_variant | Intron 2 of 7 |
Ensembl
Frequencies
GnomAD3 genomes 0.000147 AC: 16AN: 109006Hom.: 0 Cov.: 14 show subpopulations
GnomAD3 genomes
AF:
AC:
16
AN:
109006
Hom.:
Cov.:
14
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.000147 AC: 16AN: 109076Hom.: 0 Cov.: 14 AF XY: 0.000134 AC XY: 7AN XY: 52086 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
16
AN:
109076
Hom.:
Cov.:
14
AF XY:
AC XY:
7
AN XY:
52086
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
6
AN:
18066
American (AMR)
AF:
AC:
3
AN:
11668
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3008
East Asian (EAS)
AF:
AC:
1
AN:
4562
South Asian (SAS)
AF:
AC:
0
AN:
3434
European-Finnish (FIN)
AF:
AC:
0
AN:
8130
Middle Eastern (MID)
AF:
AC:
0
AN:
244
European-Non Finnish (NFE)
AF:
AC:
6
AN:
57674
Other (OTH)
AF:
AC:
0
AN:
1456
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000000000000555111), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.306
Heterozygous variant carriers
0
1
3
4
6
7
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
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6
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10
<30
30-35
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>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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