14-91273058-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001080414.4(CCDC88C):c.5654G>A(p.Arg1885His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000486 in 1,556,670 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001080414.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.5654G>A | p.Arg1885His | missense_variant | Exon 30 of 30 | 5 | NM_001080414.4 | ENSP00000374507.6 | ||
CCDC88C | ENST00000556726 | c.*1488G>A | 3_prime_UTR_variant | Exon 7 of 7 | 5 | ENSP00000452406.1 |
Frequencies
GnomAD3 genomes AF: 0.00243 AC: 370AN: 152188Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000582 AC: 93AN: 159856Hom.: 1 AF XY: 0.000354 AC XY: 31AN XY: 87514
GnomAD4 exome AF: 0.000273 AC: 384AN: 1404364Hom.: 1 Cov.: 34 AF XY: 0.000245 AC XY: 170AN XY: 693242
GnomAD4 genome AF: 0.00244 AC: 372AN: 152306Hom.: 2 Cov.: 32 AF XY: 0.00232 AC XY: 173AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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CCDC88C-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at