3-46976731-A-G
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_001277074.2(CCDC12):c.2T>C(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,453,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001277074.2 start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC12 | NM_001277074.2 | c.2T>C | p.Met1? | start_lost | Exon 1 of 7 | ENST00000683445.1 | NP_001264003.1 | |
CCDC12 | NM_144716.6 | c.41T>C | p.Met14Thr | missense_variant | Exon 2 of 8 | NP_653317.2 | ||
CCDC12 | NR_102269.2 | n.-230T>C | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1453820Hom.: 0 Cov.: 34 AF XY: 0.00000277 AC XY: 2AN XY: 722454
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.41T>C (p.M14T) alteration is located in exon 1 (coding exon 1) of the CCDC12 gene. This alteration results from a T to C substitution at nucleotide position 41, causing the methionine (M) at amino acid position 14 to be replaced by a threonine (T). 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