chr3-159252782-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001042706.3(IQCJ):c.130C>G(p.Gln44Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Consequence
IQCJ
NM_001042706.3 missense
NM_001042706.3 missense
Scores
3
10
Clinical Significance
Conservation
PhyloP100: 3.49
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.24051696).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCJ | NM_001042706.3 | c.130C>G | p.Gln44Glu | missense_variant | 3/4 | ENST00000397832.7 | |
IQCJ-SCHIP1 | NM_001197113.2 | c.130C>G | p.Gln44Glu | missense_variant | 3/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCJ | ENST00000397832.7 | c.130C>G | p.Gln44Glu | missense_variant | 3/4 | 1 | NM_001042706.3 | ||
IQCJ | ENST00000451172.5 | c.130C>G | p.Gln44Glu | missense_variant | 3/5 | 1 | P1 | ||
IQCJ | ENST00000482126.1 | c.74+6875C>G | intron_variant | 1 | |||||
IQCJ | ENST00000481796.1 | n.435+6875C>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
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 | Dec 06, 2021 | The c.130C>G (p.Q44E) alteration is located in exon 3 (coding exon 3) of the IQCJ gene. This alteration results from a C to G substitution at nucleotide position 130, causing the glutamine (Q) at amino acid position 44 to be replaced by a glutamic acid (E). 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
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;N;N;D;N
PrimateAI
Benign
T
Polyphen
0.86, 0.97
.;.;.;.;P;D
Vest4
0.46, 0.54, 0.58
MutPred
Loss of MoRF binding (P = 0.0536);Loss of MoRF binding (P = 0.0536);Loss of MoRF binding (P = 0.0536);.;Loss of MoRF binding (P = 0.0536);Loss of MoRF binding (P = 0.0536);
MVP
0.21
MPC
0.38, 0.030
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