rs1663549
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_133459.4(CCBE1):c.265+26C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,413,438 control chromosomes in the GnomAD database, including 53,500 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.28 ( 6018 hom., cov: 33)
Exomes 𝑓: 0.27 ( 47482 hom. )
Consequence
CCBE1
NM_133459.4 intron
NM_133459.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0620
Genes affected
CCBE1 (HGNC:29426): (collagen and calcium binding EGF domains 1) This gene is thought to function in extracellular matrix remodeling and migration. It is predominantly expressed in the ovary, but down regulated in ovarian cancer cell lines and primary carcinomas, suggesting its role as a tumour suppressor. Mutations in this gene have been associated with Hennekam lymphangiectasia-lymphedema syndrome, a generalized lymphatic dysplasia in humans. [provided by RefSeq, Mar 2010]
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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=-0.85).
BP6
?
Variant 18-59480160-G-T is Benign according to our data. Variant chr18-59480160-G-T is described in ClinVar as [Benign]. Clinvar id is 262350.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCBE1 | NM_133459.4 | c.265+26C>A | intron_variant | ENST00000439986.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCBE1 | ENST00000439986.9 | c.265+26C>A | intron_variant | 1 | NM_133459.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.281 AC: 42627AN: 151966Hom.: 6017 Cov.: 33
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GnomAD3 exomes AF: 0.266 AC: 65452AN: 246022Hom.: 8876 AF XY: 0.262 AC XY: 34895AN XY: 133184
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GnomAD4 exome AF: 0.268 AC: 338373AN: 1261354Hom.: 47482 Cov.: 18 AF XY: 0.267 AC XY: 170639AN XY: 638258
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GnomAD4 genome ? AF: 0.280 AC: 42652AN: 152084Hom.: 6018 Cov.: 33 AF XY: 0.276 AC XY: 20552AN XY: 74356
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
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 51% of patients studied by a panel of primary immunodeficiencies. Number of patients: 48. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
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