dbSNP rs5735: SCNN1G:p.Ile158Ile (chr16-23189527-T-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001039.4(SCNN1G):c.474T>C(p.Ile158Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 1,613,964 control chromosomes in the GnomAD database, including 76,419 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6191 hom., cov: 32)

Exomes 𝑓: 0.31 ( 70228 hom. )

Consequence

SCNN1G
NM_001039.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.0660

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]

SCNN1G links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 16-23189527-T-C is Benign according to our data. Variant chr16-23189527-T-C is described in ClinVar as [Benign]. Clinvar id is 165173.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23189527-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.066 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCNN1G	NM_001039.4 link	c.474T>C	p.Ile158Ile	synonymous_variant	Exon 3 of 13	ENST00000300061.3	NP_001030.2	P51170A5X2V1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCNN1G	ENST00000300061.3 link	c.474T>C	p.Ile158Ile	synonymous_variant	Exon 3 of 13	1	NM_001039.4	ENSP00000300061.2		P51170

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

41432

AN:

152052

Hom.:

6168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.356

Gnomad ASJ

AF:

0.295

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.362

Gnomad MID

AF:

0.299

Gnomad NFE

AF:

0.316

Gnomad OTH

AF:

0.276

GnomAD3 exomes

AF:

0.309

AC:

77716

AN:

251480

Hom.:

12901

AF XY:

0.305

AC XY:

41396

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.436

Gnomad ASJ exome

AF:

0.305

Gnomad EAS exome

AF:

0.172

Gnomad SAS exome

AF:

0.270

Gnomad FIN exome

AF:

0.367

Gnomad NFE exome

AF:

0.314

Gnomad OTH exome

AF:

0.312

GnomAD4 exome

AF:

0.306

AC:

447240

AN:

1461796

Hom.:

70228

Cov.:

AF XY:

0.305

AC XY:

221951

AN XY:

727206

show subpopulations

Gnomad4 AFR exome

AF:

0.148

Gnomad4 AMR exome

AF:

0.431

Gnomad4 ASJ exome

AF:

0.307

Gnomad4 EAS exome

AF:

0.162

Gnomad4 SAS exome

AF:

0.271

Gnomad4 FIN exome

AF:

0.369

Gnomad4 NFE exome

AF:

0.311

Gnomad4 OTH exome

AF:

0.304

GnomAD4 genome

AF:

0.273

AC:

41505

AN:

152168

Hom.:

6191

Cov.:

AF XY:

0.275

AC XY:

20417

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.158

Gnomad4 AMR

AF:

0.356

Gnomad4 ASJ

AF:

0.295

Gnomad4 EAS

AF:

0.180

Gnomad4 SAS

AF:

0.268

Gnomad4 FIN

AF:

0.362

Gnomad4 NFE

AF:

0.316

Gnomad4 OTH

AF:

0.275

Alfa

AF:

0.304

Hom.:

9261

Bravo

AF:

0.269

Asia WGS

AF:

0.274

AC:

950

AN:

3478

EpiCase

AF:

0.306

EpiControl

AF:

0.307

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 24, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 21, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Ile158Ile in exon 3 of SCNN1G: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 32.1% (2760/8600) o f European American chromosomes from a broad population by the NHLBI Exome Seque ncing Project (http://evs.gs.washington.edu/EVS; dbSNP rs5735). -

Pseudohypoaldosteronism, type IB1, autosomal recessive

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Liddle syndrome 2

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

5.1

DANN

Benign

0.59

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over