7-123479896-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178827.5(IQUB):c.1309C>T(p.Leu437Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000217 in 1,612,910 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00022 ( 1 hom. )
Consequence
IQUB
NM_178827.5 missense
NM_178827.5 missense
Scores
3
11
5
Clinical Significance
Conservation
PhyloP100: 4.79
Genes affected
IQUB (HGNC:21995): (IQ motif and ubiquitin domain containing) Predicted to be involved in cilium assembly. Predicted to act upstream of or within smoothened signaling pathway. Predicted to be active in acrosomal vesicle and motile cilium. [provided by Alliance of Genome Resources, Apr 2022]
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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=0.21929604).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IQUB | NM_178827.5 | c.1309C>T | p.Leu437Phe | missense_variant | 8/13 | ENST00000324698.11 | NP_849149.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IQUB | ENST00000324698.11 | c.1309C>T | p.Leu437Phe | missense_variant | 8/13 | 1 | NM_178827.5 | ENSP00000324882.6 | ||
IQUB | ENST00000466202.5 | c.1309C>T | p.Leu437Phe | missense_variant | 8/13 | 1 | ENSP00000417769.1 | |||
IQUB | ENST00000484508.5 | n.1309C>T | non_coding_transcript_exon_variant | 8/14 | 2 | ENSP00000417285.1 | ||||
IQUB | ENST00000469057.1 | n.1235-10512C>T | intron_variant | 2 | ENSP00000417636.1 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152044Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000255 AC: 64AN: 250636Hom.: 0 AF XY: 0.000288 AC XY: 39AN XY: 135446
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GnomAD4 exome AF: 0.000219 AC: 320AN: 1460748Hom.: 1 Cov.: 30 AF XY: 0.000226 AC XY: 164AN XY: 726710
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GnomAD4 genome AF: 0.000197 AC: 30AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74392
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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 | Apr 08, 2022 | The c.1309C>T (p.L437F) alteration is located in exon 8 (coding exon 7) of the IQUB gene. This alteration results from a C to T substitution at nucleotide position 1309, causing the leucine (L) at amino acid position 437 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
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Uncertain
T
MutationAssessor
Pathogenic
M;M
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Uncertain
Sift
Pathogenic
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at