chr10-12898561-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_031455.4(CCDC3):c.668A>T(p.Lys223Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000527 in 1,614,020 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K223E) has been classified as Uncertain significance.
Frequency
Consequence
NM_031455.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC3 | NM_031455.4 | c.668A>T | p.Lys223Met | missense_variant | 3/3 | ENST00000378825.5 | |
CCDC3 | NM_001282658.2 | c.293A>T | p.Lys98Met | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC3 | ENST00000378825.5 | c.668A>T | p.Lys223Met | missense_variant | 3/3 | 1 | NM_031455.4 | P1 | |
ENST00000649832.1 | n.560T>A | non_coding_transcript_exon_variant | 3/5 | ||||||
CCDC3 | ENST00000378839.1 | c.293A>T | p.Lys98Met | missense_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251458Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135916
GnomAD4 exome AF: 0.0000540 AC: 79AN: 1461806Hom.: 0 Cov.: 35 AF XY: 0.0000481 AC XY: 35AN XY: 727206
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.668A>T (p.K223M) alteration is located in exon 3 (coding exon 3) of the CCDC3 gene. This alteration results from a A to T substitution at nucleotide position 668, causing the lysine (K) at amino acid position 223 to be replaced by a methionine (M). 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