chr3-46976699-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001277074.2(CCDC12):āc.34G>Cā(p.Glu12Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000449 in 1,604,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001277074.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC12 | NM_001277074.2 | c.34G>C | p.Glu12Gln | missense_variant | 1/7 | ENST00000683445.1 | |
CCDC12 | NM_144716.6 | c.73G>C | p.Glu25Gln | missense_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC12 | ENST00000683445.1 | c.34G>C | p.Glu12Gln | missense_variant | 1/7 | NM_001277074.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152256Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000260 AC: 6AN: 230434Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 125070
GnomAD4 exome AF: 0.0000358 AC: 52AN: 1452440Hom.: 0 Cov.: 56 AF XY: 0.0000236 AC XY: 17AN XY: 721854
GnomAD4 genome AF: 0.000131 AC: 20AN: 152256Hom.: 0 Cov.: 35 AF XY: 0.000108 AC XY: 8AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 13, 2023 | The c.73G>C (p.E25Q) alteration is located in exon 1 (coding exon 1) of the CCDC12 gene. This alteration results from a G to C substitution at nucleotide position 73, causing the glutamic acid (E) at amino acid position 25 to be replaced by a glutamine (Q). 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