16-30183126-A-C
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The ENST00000561815.5(CORO1A):c.100A>C(p.Arg34Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 424,950 control chromosomes in the GnomAD database, including 1,054 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.017 ( 215 hom., cov: 32)
Exomes 𝑓: 0.024 ( 839 hom. )
Consequence
CORO1A
ENST00000561815.5 synonymous
ENST00000561815.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.114
Genes affected
CORO1A (HGNC:2252): (coronin 1A) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Alternative splicing results in multiple transcript variants. A related pseudogene has been defined on chromosome 16. [provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 16-30183126-A-C is Benign according to our data. Variant chr16-30183126-A-C is described in ClinVar as [Benign]. Clinvar id is 2688464.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.114 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
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Ensembl
Frequencies
GnomAD3 genomes AF: 0.0169 AC: 2562AN: 152034Hom.: 214 Cov.: 32
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GnomAD3 exomes AF: 0.0561 AC: 5628AN: 100370Hom.: 717 AF XY: 0.0424 AC XY: 2387AN XY: 56354
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GnomAD4 exome AF: 0.0242 AC: 6615AN: 272798Hom.: 839 Cov.: 0 AF XY: 0.0185 AC XY: 2905AN XY: 157432
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GnomAD4 genome AF: 0.0169 AC: 2567AN: 152152Hom.: 215 Cov.: 32 AF XY: 0.0191 AC XY: 1419AN XY: 74398
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
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 28% of patients studied by a panel of primary immunodeficiencies. Number of patients: 25. Only high quality variants are reported. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at