rs779644080
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_017721.5(CC2D1A):c.2441C>T(p.Ala814Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000818 in 1,613,552 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A814S) has been classified as Likely benign.
Frequency
Consequence
NM_017721.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CC2D1A | NM_017721.5 | c.2441C>T | p.Ala814Val | missense_variant | 23/29 | ENST00000318003.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CC2D1A | ENST00000318003.11 | c.2441C>T | p.Ala814Val | missense_variant | 23/29 | 1 | NM_017721.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152070Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249344Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135314
GnomAD4 exome AF: 0.0000842 AC: 123AN: 1461482Hom.: 0 Cov.: 36 AF XY: 0.0000715 AC XY: 52AN XY: 727062
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152070Hom.: 0 Cov.: 30 AF XY: 0.0000404 AC XY: 3AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 13, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at