rs12492214
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001023570.4(IQCB1):c.766+46T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 1,457,066 control chromosomes in the GnomAD database, including 8,554 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.10 ( 851 hom., cov: 31)
Exomes 𝑓: 0.11 ( 7703 hom. )
Consequence
IQCB1
NM_001023570.4 intron
NM_001023570.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.491
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 3-121799150-A-G is Benign according to our data. Variant chr3-121799150-A-G is described in ClinVar as [Benign]. Clinvar id is 257094.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCB1 | NM_001023570.4 | c.766+46T>C | intron_variant | ENST00000310864.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCB1 | ENST00000310864.11 | c.766+46T>C | intron_variant | 1 | NM_001023570.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.103 AC: 15628AN: 151582Hom.: 851 Cov.: 31
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GnomAD3 exomes AF: 0.102 AC: 24035AN: 235088Hom.: 1381 AF XY: 0.107 AC XY: 13626AN XY: 127866
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GnomAD4 exome AF: 0.106 AC: 137889AN: 1305366Hom.: 7703 Cov.: 18 AF XY: 0.108 AC XY: 70865AN XY: 656666
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GnomAD4 genome ? AF: 0.103 AC: 15626AN: 151700Hom.: 851 Cov.: 31 AF XY: 0.104 AC XY: 7738AN XY: 74154
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 13, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at