rs765282375
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The ENST00000318003.11(CC2D1A):c.959C>A(p.Pro320Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,612,276 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000318003.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CC2D1A | NM_017721.5 | c.959C>A | p.Pro320Gln | missense_variant | 9/29 | ENST00000318003.11 | NP_060191.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CC2D1A | ENST00000318003.11 | c.959C>A | p.Pro320Gln | missense_variant | 9/29 | 1 | NM_017721.5 | ENSP00000313601 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152186Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000158 AC: 39AN: 247050Hom.: 0 AF XY: 0.000149 AC XY: 20AN XY: 134058
GnomAD4 exome AF: 0.0000959 AC: 140AN: 1459972Hom.: 0 Cov.: 33 AF XY: 0.0000950 AC XY: 69AN XY: 726180
GnomAD4 genome AF: 0.000210 AC: 32AN: 152304Hom.: 1 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 17, 2016 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at