chr16-1979255-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_172167.3(NOXO1):c.913G>A(p.Asp305Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000729 in 1,372,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 7.3e-7 ( 0 hom. )
Consequence
NOXO1
NM_172167.3 missense
NM_172167.3 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: -0.672
Publications
0 publications found
Genes affected
NOXO1 (HGNC:19404): (NADPH oxidase organizer 1) This gene encodes an NADPH oxidase (NOX) organizer, which positively regulates NOX1 and NOX3. The protein contains a PX domain and two SH3 domains. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jun 2012]
TBL3 (HGNC:11587): (transducin beta like 3) The protein encoded by this gene has sequence similarity with members of the WD40 repeat-containing protein family. The WD40 group is a large family of proteins, which appear to have a regulatory function. It is believed that the WD40 repeats mediate protein-protein interactions and members of the family are involved in signal transduction, RNA processing, gene regulation, vesicular trafficking, cytoskeletal assembly and may play a role in the control of cytotypic differentiation. This gene has multiple polyadenylation sites. It might have multiple alternatively spliced transcript variants but the variants have not been fully described yet. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.045013458).
BP6
Variant 16-1979255-C-T is Benign according to our data. Variant chr16-1979255-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2488358.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_172167.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NOXO1 | MANE Select | c.913G>A | p.Asp305Asn | missense | Exon 8 of 8 | NP_751907.1 | Q8NFA2-3 | ||
| TBL3 | MANE Select | c.*570C>T | 3_prime_UTR | Exon 22 of 22 | NP_006444.2 | ||||
| NOXO1 | c.928G>A | p.Asp310Asn | missense | Exon 8 of 8 | NP_751908.1 | Q8NFA2-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NOXO1 | TSL:1 MANE Select | c.913G>A | p.Asp305Asn | missense | Exon 8 of 8 | ENSP00000348435.4 | Q8NFA2-3 | ||
| NOXO1 | TSL:1 | c.928G>A | p.Asp310Asn | missense | Exon 8 of 8 | ENSP00000380450.4 | Q8NFA2-1 | ||
| NOXO1 | TSL:1 | c.925G>A | p.Asp309Asn | missense | Exon 8 of 8 | ENSP00000456800.1 | Q8NFA2-2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD4 exome AF: 7.29e-7 AC: 1AN: 1372220Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 677224 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1372220
Hom.:
Cov.:
35
AF XY:
AC XY:
0
AN XY:
677224
show subpopulations
African (AFR)
AF:
AC:
0
AN:
29788
American (AMR)
AF:
AC:
0
AN:
33878
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24296
East Asian (EAS)
AF:
AC:
0
AN:
34770
South Asian (SAS)
AF:
AC:
0
AN:
78044
European-Finnish (FIN)
AF:
AC:
1
AN:
35048
Middle Eastern (MID)
AF:
AC:
0
AN:
4418
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1074850
Other (OTH)
AF:
AC:
0
AN:
57128
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
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.:
34
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of methylation at R306 (P = 0.2286)
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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
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