rs13116304
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001378615.1(CC2D2A):c.3288+41A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 1,544,902 control chromosomes in the GnomAD database, including 389,668 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.69 ( 36503 hom., cov: 31)
Exomes 𝑓: 0.71 ( 353165 hom. )
Consequence
CC2D2A
NM_001378615.1 intron
NM_001378615.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.28
Genes affected
CC2D2A (HGNC:29253): (coiled-coil and C2 domain containing 2A) This gene encodes a coiled-coil and calcium binding domain protein that appears to play a critical role in cilia formation. Mutations in this gene cause Meckel syndrome type 6, as well as Joubert syndrome type 9. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
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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=-0.96).
BP6
Variant 4-15567523-A-C is Benign according to our data. Variant chr4-15567523-A-C is described in ClinVar as [Benign]. Clinvar id is 126239.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CC2D2A | NM_001378615.1 | c.3288+41A>C | intron_variant | ENST00000424120.6 | |||
LOC124900671 | XR_007058061.1 | n.130+3208T>G | intron_variant, non_coding_transcript_variant | ||||
CC2D2A | NM_001080522.2 | c.3288+41A>C | intron_variant | ||||
CC2D2A | NM_001378617.1 | c.3141+41A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CC2D2A | ENST00000424120.6 | c.3288+41A>C | intron_variant | 5 | NM_001378615.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.691 AC: 104982AN: 151842Hom.: 36476 Cov.: 31
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GnomAD3 exomes AF: 0.710 AC: 158675AN: 223330Hom.: 56679 AF XY: 0.709 AC XY: 86115AN XY: 121408
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GnomAD4 exome AF: 0.711 AC: 990404AN: 1392940Hom.: 353165 Cov.: 21 AF XY: 0.712 AC XY: 494788AN XY: 695256
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GnomAD4 genome AF: 0.691 AC: 105050AN: 151962Hom.: 36503 Cov.: 31 AF XY: 0.690 AC XY: 51236AN XY: 74304
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ClinVar
Significance: Benign
Submissions summary: Benign:5
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 | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Meckel syndrome, type 6 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Joubert syndrome 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
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