1-42473350-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001395517.1(CCDC30):c.-91-7111C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,036,594 control chromosomes in the GnomAD database, including 12,892 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 1478 hom., cov: 32)
Exomes 𝑓: 0.16 ( 11414 hom. )
Consequence
CCDC30
NM_001395517.1 intron
NM_001395517.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.489
Genes affected
CCDC30 (HGNC:26103): (coiled-coil domain containing 30)
PPCS (HGNC:25686): (phosphopantothenoylcysteine synthetase) Biosynthesis of coenzyme A (CoA) from pantothenic acid (vitamin B5) is an essential universal pathway in prokaryotes and eukaryotes. PPCS (EC 6.3.2.5), one of the last enzymes in this pathway, converts phosphopantothenate to phosphopantothenoylcysteine (Daugherty et al., 2002 [PubMed 11923312]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 1-42473350-C-G is Benign according to our data. Variant chr1-42473350-C-G is described in ClinVar as [Benign]. Clinvar id is 1263588.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC30 | NM_001395517.1 | c.-91-7111C>G | intron_variant | ENST00000657597.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC30 | ENST00000657597.2 | c.-91-7111C>G | intron_variant | NM_001395517.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.130 AC: 19803AN: 152076Hom.: 1481 Cov.: 32
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GnomAD4 exome AF: 0.163 AC: 144077AN: 884400Hom.: 11414 Cov.: 12 AF XY: 0.162 AC XY: 68484AN XY: 422502
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GnomAD4 genome ? AF: 0.130 AC: 19800AN: 152194Hom.: 1478 Cov.: 32 AF XY: 0.128 AC XY: 9486AN XY: 74390
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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 14, 2021 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at