rs80008675
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_133459.4(CCBE1):c.123C>T(p.Asp41=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000859 in 1,396,488 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: 33)
Exomes 𝑓: 0.0000086 ( 0 hom. )
Consequence
CCBE1
NM_133459.4 synonymous
NM_133459.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.85
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 Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 18-59697220-G-A is Benign according to our data. Variant chr18-59697220-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1548860.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCBE1 | NM_133459.4 | c.123C>T | p.Asp41= | synonymous_variant | 1/11 | ENST00000439986.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCBE1 | ENST00000439986.9 | c.123C>T | p.Asp41= | synonymous_variant | 1/11 | 1 | NM_133459.4 | P1 | |
ENST00000588946.2 | n.212-22G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome AF: 0.00000859 AC: 12AN: 1396488Hom.: 0 Cov.: 31 AF XY: 0.00000581 AC XY: 4AN XY: 688742
GnomAD4 exome
AF:
AC:
12
AN:
1396488
Hom.:
Cov.:
31
AF XY:
AC XY:
4
AN XY:
688742
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
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
Publications
No publications associated with this variant yet.