chr7-45000161-G-GGGCCTGCTCT
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NR_030770.2(CCM2):n.112+304_112+305insGGCCTGCTCT variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 1.0 ( 56376 hom., cov: 0)
Exomes 𝑓: 0.99 ( 4423 hom. )
Failed GnomAD Quality Control
Consequence
CCM2
NR_030770.2 intron, non_coding_transcript
NR_030770.2 intron, non_coding_transcript
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.25
Genes affected
CCM2 (HGNC:21708): (CCM2 scaffold protein) This gene encodes a scaffold protein that functions in the stress-activated p38 Mitogen-activated protein kinase (MAPK) signaling cascade. The protein interacts with SMAD specific E3 ubiquitin protein ligase 1 (also known as SMURF1) via a phosphotyrosine binding domain to promote RhoA degradation. The protein is required for normal cytoskeletal structure, cell-cell interactions, and lumen formation in endothelial cells. Mutations in this gene result in cerebral cavernous malformations. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 7-45000161-G-GGGCCTGCTCT is Benign according to our data. Variant chr7-45000161-G-GGGCCTGCTCT is described in ClinVar as [Benign]. Clinvar id is 1266041.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCM2 | NM_031443.4 | upstream_gene_variant | ENST00000258781.11 | NP_113631.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCM2 | ENST00000258781.11 | upstream_gene_variant | 1 | NM_031443.4 | ENSP00000258781 | P1 |
Frequencies
GnomAD3 genomes AF: 0.997 AC: 112967AN: 113264Hom.: 56339 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.994 AC: 8894AN: 8944Hom.: 4423 Cov.: 3 AF XY: 0.996 AC XY: 4535AN XY: 4554
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GnomAD4 genome AF: 0.997 AC: 113040AN: 113336Hom.: 56376 Cov.: 0 AF XY: 0.998 AC XY: 53440AN XY: 53564
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at