12-122774680-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_201435.5(CCDC62):c.10C>A(p.Pro4Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000159 in 1,255,658 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_201435.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC62 | ENST00000253079.11 | c.10C>A | p.Pro4Thr | missense_variant | Exon 1 of 13 | 1 | NM_201435.5 | ENSP00000253079.6 | ||
CCDC62 | ENST00000392441.8 | c.10C>A | p.Pro4Thr | missense_variant | Exon 1 of 12 | 5 | ENSP00000376236.4 | |||
CCDC62 | ENST00000539171.1 | c.10C>A | p.Pro4Thr | missense_variant | Exon 1 of 3 | 3 | ENSP00000439893.1 | |||
CCDC62 | ENST00000341952.8 | n.10C>A | non_coding_transcript_exon_variant | Exon 1 of 13 | 2 | ENSP00000341471.4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152016Hom.: 0 Cov.: 31
GnomAD4 exome AF: 9.06e-7 AC: 1AN: 1103526Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 522680
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.10C>A (p.P4T) alteration is located in exon 1 (coding exon 1) of the CCDC62 gene. This alteration results from a C to A substitution at nucleotide position 10, causing the proline (P) at amino acid position 4 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