16-23206081-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000300061.3(SCNN1G):​c.1078-3669C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,168 control chromosomes in the GnomAD database, including 2,775 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.18 ( 2775 hom., cov: 32)

Consequence

SCNN1G
ENST00000300061.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.61
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SCNN1GNM_001039.4 linkuse as main transcriptc.1078-3669C>T intron_variant ENST00000300061.3 NP_001030.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SCNN1GENST00000300061.3 linkuse as main transcriptc.1078-3669C>T intron_variant 1 NM_001039.4 ENSP00000300061 P1
ENST00000563471.1 linkuse as main transcriptn.101+6923G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.183
AC:
27877
AN:
152050
Hom.:
2766
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.119
Gnomad AMI
AF:
0.307
Gnomad AMR
AF:
0.242
Gnomad ASJ
AF:
0.191
Gnomad EAS
AF:
0.0986
Gnomad SAS
AF:
0.247
Gnomad FIN
AF:
0.194
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.207
Gnomad OTH
AF:
0.190
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.183
AC:
27912
AN:
152168
Hom.:
2775
Cov.:
32
AF XY:
0.182
AC XY:
13509
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.119
Gnomad4 AMR
AF:
0.243
Gnomad4 ASJ
AF:
0.191
Gnomad4 EAS
AF:
0.0986
Gnomad4 SAS
AF:
0.250
Gnomad4 FIN
AF:
0.194
Gnomad4 NFE
AF:
0.207
Gnomad4 OTH
AF:
0.188
Alfa
AF:
0.178
Hom.:
1053
Bravo
AF:
0.187
Asia WGS
AF:
0.171
AC:
591
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.12
DANN
Benign
0.49

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4401050; hg19: chr16-23217402; API