chr19-13927918-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_017721.5(CC2D1A):c.2342G>A(p.Gly781Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000243 in 1,613,626 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. G781A) 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 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CC2D1A | NM_017721.5 | c.2342G>A | p.Gly781Glu | missense_variant | 23/29 | ENST00000318003.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CC2D1A | ENST00000318003.11 | c.2342G>A | p.Gly781Glu | missense_variant | 23/29 | 1 | NM_017721.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152132Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000121 AC: 30AN: 248696Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135078
GnomAD4 exome AF: 0.000250 AC: 365AN: 1461376Hom.: 0 Cov.: 32 AF XY: 0.000227 AC XY: 165AN XY: 727000
GnomAD4 genome AF: 0.000177 AC: 27AN: 152250Hom.: 0 Cov.: 30 AF XY: 0.000161 AC XY: 12AN XY: 74454
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2018 | The p.G781E variant (also known as c.2342G>A), located in coding exon 23 of the CC2D1A gene, results from a G to A substitution at nucleotide position 2342. The glycine at codon 781 is replaced by glutamic acid, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at