chr10-13001528-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031455.4(CCDC3):c.43C>G(p.Pro15Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000945 in 1,312,396 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P15T) has been classified as Uncertain significance.
Frequency
Consequence
NM_031455.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC3 | NM_031455.4 | c.43C>G | p.Pro15Ala | missense_variant | 1/3 | ENST00000378825.5 | |
CCDC3 | NM_001282658.2 | c.-1-3016C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC3 | ENST00000378825.5 | c.43C>G | p.Pro15Ala | missense_variant | 1/3 | 1 | NM_031455.4 | P1 | |
CCDC3 | ENST00000378839.1 | c.-1-3016C>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000990 AC: 15AN: 151476Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000939 AC: 109AN: 1160920Hom.: 0 Cov.: 33 AF XY: 0.0000772 AC XY: 43AN XY: 556918
GnomAD4 genome ? AF: 0.0000990 AC: 15AN: 151476Hom.: 0 Cov.: 32 AF XY: 0.0000946 AC XY: 7AN XY: 73966
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.43C>G (p.P15A) alteration is located in exon 1 (coding exon 1) of the CCDC3 gene. This alteration results from a C to G substitution at nucleotide position 43, causing the proline (P) at amino acid position 15 to be replaced by an alanine (A). 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