3-46979634-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_144716.6(CCDC12):c.-73+2298T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 305,436 control chromosomes in the GnomAD database, including 44,634 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.49 ( 19812 hom., cov: 33)
Exomes 𝑓: 0.57 ( 24822 hom. )
Consequence
CCDC12
NM_144716.6 intron
NM_144716.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.71
Genes affected
CCDC12 (HGNC:28332): (coiled-coil domain containing 12) Predicted to be part of U2-type spliceosomal complex and post-mRNA release spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]
NBEAL2 (HGNC:31928): (neurobeachin like 2) The protein encoded by this gene contains a beige and Chediak-Higashi (BEACH) domain and multiple WD40 domains, and may play a role in megakaryocyte alpha-granule biogenesis. Mutations in this gene are a cause of gray platelet syndrome. [provided by RefSeq, Dec 2011]
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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=-0.72).
BP6
Variant 3-46979634-A-G is Benign according to our data. Variant chr3-46979634-A-G is described in ClinVar as [Benign]. Clinvar id is 1248264.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NBEAL2 | NM_015175.3 | upstream_gene_variant | ENST00000450053.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NBEAL2 | ENST00000450053.8 | upstream_gene_variant | 2 | NM_015175.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.491 AC: 74589AN: 151926Hom.: 19788 Cov.: 33
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GnomAD4 exome AF: 0.566 AC: 86808AN: 153390Hom.: 24822 Cov.: 0 AF XY: 0.567 AC XY: 44750AN XY: 78986
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GnomAD4 genome AF: 0.491 AC: 74646AN: 152046Hom.: 19812 Cov.: 33 AF XY: 0.492 AC XY: 36582AN XY: 74334
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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