Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_017721.5(CC2D1A):c.2402C>T(p.Thr801Met) variant causes a missense change. The variant allele was found at a frequency of 0.246 in 1,613,272 control chromosomes in the GnomAD database, including 52,801 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
CC2D1A (HGNC:30237): (coiled-coil and C2 domain containing 1A) This gene encodes a transcriptional repressor that binds to a conserved 14-bp 5'-repressor element and regulates expression of the 5-hydroxytryptamine (serotonin) receptor 1A gene in neuronal cells. The DNA binding and transcriptional repressor activities of the protein are inhibited by calcium. A mutation in this gene results in a nonsyndromic form of cognitive disability (MRT3). [provided by RefSeq, Jul 2017]
CC2D1A Gene-Disease associations (from GenCC):
complex neurodevelopmental disorder
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0016435385).
BP6
Variant 19-13927978-C-T is Benign according to our data. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13927978-C-T is described in CliVar as Benign. Clinvar id is 128619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.
Genetic Services Laboratory, University of Chicago
Significance:Likely benign
Review Status:no assertion criteria provided
Collection Method:clinical testing
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Inborn genetic diseasesBenign:1
Mar 17, 2016
Ambry Genetics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
This alteration is classified as 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. -