NM_001023570.4:c.1410+18C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001023570.4(IQCB1):c.1410+18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,455,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
IQCB1
NM_001023570.4 intron
NM_001023570.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0160
Publications
0 publications found
Genes affected
IQCB1 (HGNC:28949): (IQ motif containing B1) This gene encodes a nephrocystin protein that interacts with calmodulin and the retinitis pigmentosa GTPase regulator protein. The encoded protein has a central coiled-coil region and two calmodulin-binding IQ domains. It is localized to the primary cilia of renal epithelial cells and connecting cilia of photoreceptor cells. The protein is thought to play a role in ciliary function. Defects in this gene result in Senior-Loken syndrome type 5. Alternative splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 6. [provided by RefSeq, Jan 2016]
IQCB1 Gene-Disease associations (from GenCC):
- Senior-Loken syndrome 5Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- Leber congenital amaurosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Senior-Loken syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 3-121781725-G-A is Benign according to our data. Variant chr3-121781725-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 257091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IQCB1 | ENST00000310864.11 | c.1410+18C>T | intron_variant | Intron 13 of 14 | 1 | NM_001023570.4 | ENSP00000311505.6 | |||
IQCB1 | ENST00000349820.10 | c.1011+18C>T | intron_variant | Intron 10 of 11 | 1 | ENSP00000323756.7 | ||||
IQCB1 | ENST00000393650.7 | n.*388+18C>T | intron_variant | Intron 12 of 13 | 5 | ENSP00000377261.3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1455176Hom.: 0 Cov.: 31 AF XY: 0.00000414 AC XY: 3AN XY: 724230 show subpopulations
GnomAD4 exome
AF:
AC:
5
AN:
1455176
Hom.:
Cov.:
31
AF XY:
AC XY:
3
AN XY:
724230
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33324
American (AMR)
AF:
AC:
0
AN:
44642
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26016
East Asian (EAS)
AF:
AC:
0
AN:
39562
South Asian (SAS)
AF:
AC:
3
AN:
86006
European-Finnish (FIN)
AF:
AC:
0
AN:
53218
Middle Eastern (MID)
AF:
AC:
0
AN:
5746
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1106578
Other (OTH)
AF:
AC:
0
AN:
60084
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.515
Heterozygous variant carriers
0
1
1
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2
3
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0.20
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0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
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>80
Age
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Nephronophthisis Benign:1
May 25, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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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