16-23185981-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001039.4(SCNN1G):c.-44-247C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,964 control chromosomes in the GnomAD database, including 3,407 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.19 ( 3407 hom., cov: 33)
Consequence
SCNN1G
NM_001039.4 intron
NM_001039.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0780
Genes affected
SCNN1G (HGNC:10602): (sodium channel epithelial 1 subunit gamma) 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 gamma subunit, and mutations in this gene have been associated with Liddle syndrome. [provided by RefSeq, Apr 2009]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 16-23185981-C-T is Benign according to our data. Variant chr16-23185981-C-T is described in ClinVar as [Benign]. Clinvar id is 1283927.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.194 AC: 29518AN: 151844Hom.: 3390 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
29518
AN:
151844
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.195 AC: 29561AN: 151964Hom.: 3407 Cov.: 33 AF XY: 0.196 AC XY: 14526AN XY: 74300 show subpopulations
GnomAD4 genome
AF:
AC:
29561
AN:
151964
Hom.:
Cov.:
33
AF XY:
AC XY:
14526
AN XY:
74300
Gnomad4 AFR
AF:
AC:
0.0774242
AN:
0.0774242
Gnomad4 AMR
AF:
AC:
0.297698
AN:
0.297698
Gnomad4 ASJ
AF:
AC:
0.244528
AN:
0.244528
Gnomad4 EAS
AF:
AC:
0.148141
AN:
0.148141
Gnomad4 SAS
AF:
AC:
0.217662
AN:
0.217662
Gnomad4 FIN
AF:
AC:
0.239721
AN:
0.239721
Gnomad4 NFE
AF:
AC:
0.233022
AN:
0.233022
Gnomad4 OTH
AF:
AC:
0.201231
AN:
0.201231
Heterozygous variant carriers
0
1211
2423
3634
4846
6057
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
322
644
966
1288
1610
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
628
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Nov 12, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at