Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000336.3(SCNN1B):c.1543-17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00822 in 1,614,002 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
SCNN1B (HGNC:10600): (sodium channel epithelial 1 subunit beta) Nonvoltage-gated, amiloride-sensitive, sodium channels control fluid and electrolyte transport across epithelia in many organs. These channels are heteromeric complexes consisting of 3 subunits: alpha, beta, and gamma. This gene encodes the beta subunit, and mutations in this gene have been associated with pseudohypoaldosteronism type 1 (PHA1), and Liddle syndrome. [provided by RefSeq, Apr 2009]
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 16-23380404-C-T is Benign according to our data. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23380404-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 255866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00704 (1072/152330) while in subpopulation NFE AF = 0.0103 (700/68024). AF 95% confidence interval is 0.00966. There are 10 homozygotes in GnomAd4. There are 518 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.