3-46923627-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001277074.2(CCDC12):c.286G>A(p.Glu96Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000151 in 1,589,294 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001277074.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC12 | NM_001277074.2 | c.286G>A | p.Glu96Lys | missense_variant | Exon 4 of 7 | ENST00000683445.1 | NP_001264003.1 | |
CCDC12 | NM_144716.6 | c.325G>A | p.Glu109Lys | missense_variant | Exon 5 of 8 | NP_653317.2 | ||
CCDC12 | NR_102269.2 | n.339G>A | non_coding_transcript_exon_variant | Exon 4 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000537 AC: 12AN: 223622Hom.: 0 AF XY: 0.0000333 AC XY: 4AN XY: 120278
GnomAD4 exome AF: 0.0000139 AC: 20AN: 1436974Hom.: 0 Cov.: 30 AF XY: 0.0000126 AC XY: 9AN XY: 713000
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.325G>A (p.E109K) alteration is located in exon 4 (coding exon 4) of the CCDC12 gene. This alteration results from a G to A substitution at nucleotide position 325, causing the glutamic acid (E) at amino acid position 109 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at