3-28338017-G-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_022461.5(AZI2):c.359C>T(p.Ser120Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000209 in 1,433,796 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
AZI2
NM_022461.5 missense
NM_022461.5 missense
Scores
2
10
7
Clinical Significance
Conservation
PhyloP100: 3.86
Genes affected
AZI2 (HGNC:24002): (5-azacytidine induced 2) AZI2, or NAP1, contributes to the activation of NFKB (see MIM 164011)-dependent gene expression by activating IKK-related kinases, such as NAK (TBK1; MIM 604834) (Fujita et al., 2003 [PubMed 14560022]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AZI2 | NM_022461.5 | c.359C>T | p.Ser120Phe | missense_variant | 4/8 | ENST00000479665.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AZI2 | ENST00000479665.6 | c.359C>T | p.Ser120Phe | missense_variant | 4/8 | 2 | NM_022461.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000209 AC: 3AN: 1433796Hom.: 0 Cov.: 28 AF XY: 0.00000140 AC XY: 1AN XY: 712964
GnomAD4 exome
AF:
AC:
3
AN:
1433796
Hom.:
Cov.:
28
AF XY:
AC XY:
1
AN XY:
712964
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2021 | The c.359C>T (p.S120F) alteration is located in exon 4 (coding exon 3) of the AZI2 gene. This alteration results from a C to T substitution at nucleotide position 359, causing the serine (S) at amino acid position 120 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;.;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;M;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Uncertain
Sift
Benign
T;D;D;D;D
Sift4G
Uncertain
D;D;D;D;.
Polyphen
P;.;.;.;D
Vest4
MutPred
Gain of glycosylation at S118 (P = 0.01);Gain of glycosylation at S118 (P = 0.01);Gain of glycosylation at S118 (P = 0.01);Gain of glycosylation at S118 (P = 0.01);Gain of glycosylation at S118 (P = 0.01);
MVP
MPC
ClinPred
D
GERP RS
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