15-90230550-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006384.4(CIB1):c.555-45G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 1,548,520 control chromosomes in the GnomAD database, including 199,009 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.49 ( 18632 hom., cov: 32)
Exomes 𝑓: 0.50 ( 180377 hom. )
Consequence
CIB1
NM_006384.4 intron
NM_006384.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.65
Genes affected
CIB1 (HGNC:16920): (calcium and integrin binding 1) This gene encodes a member of the EF-hand domain-containing calcium-binding superfamily. The encoded protein interacts with many other proteins, including the platelet integrin alpha-IIb-beta-3, DNA-dependent protein kinase, presenilin-2, focal adhesion kinase, p21 activated kinase, and protein kinase D. The encoded protein may be involved in cell survival and proliferation, and is associated with several disease states including cancer and Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 15-90230550-C-T is Benign according to our data. Variant chr15-90230550-C-T is described in ClinVar as [Benign]. Clinvar id is 2688352.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CIB1 | NM_006384.4 | c.555-45G>A | intron_variant | ENST00000328649.11 | NP_006375.2 | |||
CIB1 | NM_001277764.2 | c.675-45G>A | intron_variant | NP_001264693.1 | ||||
CIB1 | NR_102427.1 | n.741-45G>A | intron_variant, non_coding_transcript_variant | |||||
CIB1 | NR_102428.1 | n.607-45G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CIB1 | ENST00000328649.11 | c.555-45G>A | intron_variant | 1 | NM_006384.4 | ENSP00000333873 | P1 |
Frequencies
GnomAD3 genomes AF: 0.487 AC: 73946AN: 151900Hom.: 18621 Cov.: 32
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GnomAD3 exomes AF: 0.555 AC: 86289AN: 155574Hom.: 25059 AF XY: 0.559 AC XY: 45794AN XY: 81904
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GnomAD4 exome AF: 0.503 AC: 702442AN: 1396502Hom.: 180377 Cov.: 32 AF XY: 0.507 AC XY: 349286AN XY: 688972
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GnomAD4 genome AF: 0.487 AC: 73989AN: 152018Hom.: 18632 Cov.: 32 AF XY: 0.497 AC XY: 36918AN XY: 74310
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 80% of patients studied by a panel of primary immunodeficiencies. Number of patients: 70. Only high quality variants are reported. - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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