chr14-91272677-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001080414.4(CCDC88C):c.6035C>T(p.Pro2012Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,611,428 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 (★). Synonymous variant affecting the same amino acid position (i.e. P2012P) has been classified as Likely benign.
Frequency
Consequence
NM_001080414.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88C | NM_001080414.4 | c.6035C>T | p.Pro2012Leu | missense_variant | 30/30 | ENST00000389857.11 | |
CCDC88C | XM_011536796.3 | c.5927C>T | p.Pro1976Leu | missense_variant | 30/30 | ||
CCDC88C | XM_047431418.1 | c.5768C>T | p.Pro1923Leu | missense_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.6035C>T | p.Pro2012Leu | missense_variant | 30/30 | 5 | NM_001080414.4 | P1 | |
CCDC88C | ENST00000556726.5 | c.*1869C>T | 3_prime_UTR_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000413 AC: 10AN: 242324Hom.: 0 AF XY: 0.0000377 AC XY: 5AN XY: 132788
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1459236Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 12AN XY: 725960
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
Spinocerebellar ataxia type 40 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics | Sep 08, 2021 | A heterozygous missense variation in exon 30 of the CCDC88C gene that results in the amino acid substitution of leucine for proline at codon 2012 was detected. The observed variant c.6035C>T (p.Pro2012Leu) has not been reported in the 1000 genomes and has a minor allele frequency of 0.003% in the gnomAD database. The in silico prediction of the variant are possibly damaging by PolyPhen-2 (HumDiv) and damaging by SIFT and MutationTaster2. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as a variant of uncertain significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at