12-122774705-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000253079.11(CCDC62):c.35A>T(p.Gln12Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000621 in 1,255,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000253079.11 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC62 | NM_201435.5 | c.35A>T | p.Gln12Leu | missense_variant, splice_region_variant | 1/13 | ENST00000253079.11 | NP_958843.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC62 | ENST00000253079.11 | c.35A>T | p.Gln12Leu | missense_variant, splice_region_variant | 1/13 | 1 | NM_201435.5 | ENSP00000253079 | P3 | |
CCDC62 | ENST00000392441.8 | c.35A>T | p.Gln12Leu | missense_variant, splice_region_variant | 1/12 | 5 | ENSP00000376236 | A2 | ||
CCDC62 | ENST00000539171.1 | c.35A>T | p.Gln12Leu | missense_variant, splice_region_variant | 1/3 | 3 | ENSP00000439893 | |||
CCDC62 | ENST00000341952.8 | c.35A>T | p.Gln12Leu | missense_variant, splice_region_variant, NMD_transcript_variant | 1/13 | 2 | ENSP00000341471 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152006Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000698 AC: 77AN: 1103688Hom.: 0 Cov.: 30 AF XY: 0.0000708 AC XY: 37AN XY: 522798
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152006Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2022 | The c.35A>T (p.Q12L) alteration is located in exon 1 (coding exon 1) of the CCDC62 gene. This alteration results from a A to T substitution at nucleotide position 35, causing the glutamine (Q) at amino acid position 12 to be replaced by a leucine (L). 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