chr3-46979345-A-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_144716.6(CCDC12):c.-72-2502T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.946 in 152,382 control chromosomes in the GnomAD database, including 68,686 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.95 ( 68624 hom., cov: 34)
Exomes 𝑓: 0.99 ( 62 hom. )
Consequence
CCDC12
NM_144716.6 intron
NM_144716.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.669
Genes affected
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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=-0.83).
BP6
Variant 3-46979345-A-T is Benign according to our data. Variant chr3-46979345-A-T is described in ClinVar as [Benign]. Clinvar id is 1288588.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC12 | NM_144716.6 | c.-72-2502T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC12 | ENST00000292314.6 | c.-72-2502T>A | intron_variant | 5 | |||||
CCDC12 | ENST00000425441.5 | c.-214-2305T>A | intron_variant | 5 | P1 | ||||
CCDC12 | ENST00000446836.5 | c.-111-2502T>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.946 AC: 143862AN: 152138Hom.: 68580 Cov.: 34
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GnomAD4 exome AF: 0.992 AC: 125AN: 126Hom.: 62 AF XY: 0.988 AC XY: 81AN XY: 82
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GnomAD4 genome AF: 0.946 AC: 143966AN: 152256Hom.: 68624 Cov.: 34 AF XY: 0.948 AC XY: 70550AN XY: 74438
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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 | Jun 19, 2021 | - - |
Computational scores
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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