14-91307150-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001080414.4(CCDC88C):c.3083C>T(p.Ala1028Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,613,634 control chromosomes in the GnomAD database, including 16,496 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. A1028A) has been classified as Likely 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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88C | NM_001080414.4 | c.3083C>T | p.Ala1028Val | missense_variant | 18/30 | ENST00000389857.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.3083C>T | p.Ala1028Val | missense_variant | 18/30 | 5 | NM_001080414.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.139 AC: 21196AN: 152006Hom.: 1509 Cov.: 32
GnomAD3 exomes AF: 0.160 AC: 39826AN: 248940Hom.: 3433 AF XY: 0.161 AC XY: 21801AN XY: 135106
GnomAD4 exome AF: 0.138 AC: 202394AN: 1461508Hom.: 14986 Cov.: 33 AF XY: 0.141 AC XY: 102607AN XY: 727046
GnomAD4 genome AF: 0.139 AC: 21218AN: 152126Hom.: 1510 Cov.: 32 AF XY: 0.146 AC XY: 10840AN XY: 74370
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 26, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 08, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at