1-42545489-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001395517.1(CCDC30):c.800C>A(p.Thr267Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,603,658 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_001395517.1 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 |
---|---|---|---|---|---|---|---|
CCDC30 | NM_001395517.1 | c.800C>A | p.Thr267Lys | missense_variant | 9/21 | ENST00000657597.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC30 | ENST00000657597.2 | c.800C>A | p.Thr267Lys | missense_variant | 9/21 | NM_001395517.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152014Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000125 AC: 3AN: 240546Hom.: 0 AF XY: 0.00000767 AC XY: 1AN XY: 130412
GnomAD4 exome AF: 0.0000289 AC: 42AN: 1451644Hom.: 0 Cov.: 30 AF XY: 0.0000277 AC XY: 20AN XY: 722016
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152014Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74234
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2023 | The c.335C>A (p.T112K) alteration is located in exon 4 (coding exon 3) of the CCDC30 gene. This alteration results from a C to A substitution at nucleotide position 335, causing the threonine (T) at amino acid position 112 to be replaced by a lysine (K). 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