chr10-12898480-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031455.4(CCDC3):c.749C>T(p.Ala250Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,613,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.749C>T | p.Ala250Val | missense_variant | 3/3 | ENST00000378825.5 | |
CCDC3 | NM_001282658.2 | c.374C>T | p.Ala125Val | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC3 | ENST00000378825.5 | c.749C>T | p.Ala250Val | missense_variant | 3/3 | 1 | NM_031455.4 | P1 | |
ENST00000649832.1 | n.511-32G>A | intron_variant, non_coding_transcript_variant | |||||||
CCDC3 | ENST00000378839.1 | c.374C>T | p.Ala125Val | missense_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000600 AC: 15AN: 249816Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135428
GnomAD4 exome AF: 0.000120 AC: 175AN: 1460924Hom.: 0 Cov.: 35 AF XY: 0.000105 AC XY: 76AN XY: 726740
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.749C>T (p.A250V) alteration is located in exon 3 (coding exon 3) of the CCDC3 gene. This alteration results from a C to T substitution at nucleotide position 749, causing the alanine (A) at amino acid position 250 to be replaced by a valine (V). 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