rs2539149
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020879.3(CCDC146):c.-12+14005A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000145 in 138,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000014 ( 0 hom., cov: 31)
Consequence
CCDC146
NM_020879.3 intron
NM_020879.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.221
Genes affected
CCDC146 (HGNC:29296): (coiled-coil domain containing 146) Located in centriole. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC146 | NM_020879.3 | c.-12+14005A>C | intron_variant | ENST00000285871.5 | |||
LOC124901678 | XR_007060391.1 | n.847-8011T>G | intron_variant, non_coding_transcript_variant | ||||
CCDC146 | XM_047420662.1 | c.-141+14005A>C | intron_variant | ||||
CCDC146 | XM_047420664.1 | c.-10+14005A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC146 | ENST00000285871.5 | c.-12+14005A>C | intron_variant | 1 | NM_020879.3 | P1 | |||
CCDC146 | ENST00000415750.5 | c.-12+14269A>C | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000145 AC: 2AN: 138158Hom.: 0 Cov.: 31
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0000145 AC: 2AN: 138158Hom.: 0 Cov.: 31 AF XY: 0.0000149 AC XY: 1AN XY: 67148
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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