Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001127198.5(TMC6):c.1950C>T(p.Thr650Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,606,306 control chromosomes in the GnomAD database, including 18,870 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T650T) has been classified as Likely benign.
TMC6 (HGNC:18021): (transmembrane channel like 6) Epidermodysplasia verruciformis (EV) is an autosomal recessive dermatosis characterized by abnormal susceptibility to human papillomaviruses (HPVs) and a high rate of progression to squamous cell carcinoma on sun-exposed skin. EV is caused by mutations in either of two adjacent genes located on chromosome 17q25.3. Both of these genes encode integral membrane proteins that localize to the endoplasmic reticulum and are predicted to form transmembrane channels. This gene encodes a transmembrane channel-like protein with 10 transmembrane domains and 2 leucine zipper motifs. [provided by RefSeq, Jul 2008]
TMC6 Gene-Disease associations (from GenCC):
epidermodysplasia verruciformis, susceptibility to, 1
Our verdict: Benign. The variant received -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 17-78117873-G-A is Benign according to our data. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-78117873-G-A is described in CliVar as Benign. Clinvar id is 1165515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.093 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.
Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
Jul 09, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
not specifiedBenign:1
Jan 24, 2024
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
This variant is classified as Benign based on local population frequency. This variant was detected in 24% of patients studied by a panel of primary immunodeficiencies. Number of patients: 23. Only high quality variants are reported. -