chr14-91272667-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001080414.4(CCDC88C):c.6045C>T(p.Gly2015=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,611,424 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G2015G) has been classified as Likely benign.
Frequency
Consequence
NM_001080414.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88C | NM_001080414.4 | c.6045C>T | p.Gly2015= | synonymous_variant | 30/30 | ENST00000389857.11 | |
CCDC88C | XM_011536796.3 | c.5937C>T | p.Gly1979= | synonymous_variant | 30/30 | ||
CCDC88C | XM_047431418.1 | c.5778C>T | p.Gly1926= | synonymous_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.6045C>T | p.Gly2015= | synonymous_variant | 30/30 | 5 | NM_001080414.4 | P1 | |
CCDC88C | ENST00000556726.5 | c.*1879C>T | 3_prime_UTR_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000413 AC: 1AN: 242368Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132854
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1459206Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 725956
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at