chr19-13927918-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP3BP4_StrongBP6BS2
The NM_017721.5(CC2D1A):c.2342G>T(p.Gly781Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000376 in 1,613,626 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CC2D1A | NM_017721.5 | c.2342G>T | p.Gly781Val | missense_variant | 23/29 | ENST00000318003.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CC2D1A | ENST00000318003.11 | c.2342G>T | p.Gly781Val | missense_variant | 23/29 | 1 | NM_017721.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000473 AC: 72AN: 152132Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00123 AC: 307AN: 248696Hom.: 2 AF XY: 0.00122 AC XY: 165AN XY: 135078
GnomAD4 exome AF: 0.000366 AC: 535AN: 1461376Hom.: 2 Cov.: 32 AF XY: 0.000366 AC XY: 266AN XY: 727000
GnomAD4 genome AF: 0.000473 AC: 72AN: 152250Hom.: 0 Cov.: 30 AF XY: 0.000484 AC XY: 36AN XY: 74454
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2018 | The p.G781V variant (also known as c.2342G>T), located in coding exon 23 of the CC2D1A gene, results from a G to T substitution at nucleotide position 2342. The glycine at codon 781 is replaced by valine, an amino acid with dissimilar 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. - |
CC2D1A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 07, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at