VCV000666751.5 - ClinVar

NM_001038.6(SCNN1A):c.1554A>G (p.Arg518=)

Germline

Classification

criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.

Likely benign

2 out of 2 submissions contributed to this classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001038.6(SCNN1A):c.1554A>G (p.Arg518=)

Variation ID: 666751 Accession: VCV000666751.5

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 12p13.31 12: 6348802 (GRCh38) [ NCBI UCSC ] 12: 6457968 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Aug 26, 2019	Dec 31, 2022	May 6, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001038.6:c.1554A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001029.1:p.Arg518=	synonymous
NM_001159575.2:c.1623A>G	NP_001153047.1:p.Arg541=	synonymous
NM_001159576.2:c.1731A>G	NP_001153048.1:p.Arg577=	synonymous
NC_000012.12:g.6348802T>C
NC_000012.11:g.6457968T>C
NG_011945.2:g.33556A>G

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000012.12:6348801:T:C

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.00020 (C)

Allele frequency Help The frequency of the allele represented by this VCV record.

Exome Aggregation Consortium (ExAC) 0.00002

The Genome Aggregation Database (gnomAD), exomes 0.00002

The Genome Aggregation Database (gnomAD) 0.00009

The Genome Aggregation Database (gnomAD) 0.00010

1000 Genomes Project 30x 0.00016

Trans-Omics for Precision Medicine (TOPMed) 0.00016

1000 Genomes Project 0.00020

Links

ClinGen: CA6405776 dbSNP: rs570566104 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
SCNN1A		-	-	GRCh38 GRCh37	422	495

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not specified	Likely benign (1)	criteria provided, single submitter	Jul 5, 2018	RCV000825232.4
Bronchiectasis with or without elevated sweat chloride 2 Liddle syndrome 3 Pseudohypoaldosteronism, type IB1, autosomal recessive	Likely benign (1)	criteria provided, single submitter	May 6, 2022	RCV002501153.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	Expand all rows Collapse all rows Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely benign (Jul 05, 2018) C Contributing to aggregate classification	criteria provided, single submitter (LMM Criteria)	not specified	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine Accession: SCV000966515.1 First in ClinVar: Aug 26, 2019 Last updated: Aug 26, 2019	Comment: show The p.Arg577Arg variant in SCNN1A is classified as likely benign because it does not alter an amino acid residue, it is not located within the splice consensus sequence, and splice prediction algorithms do not predict a newly created splice site. It has been identified in 6/24000 African chromosomes by the Genome Aggre gation Database (gnomAD, http://gnomad.broadinstitute.org). ACMG/AMP Criteria ap plied: BP4, BP7. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: not provided more Observation 1 Collection method: clinical testing Allele origin: germline Affected status: not provided Number of individuals with the variant: 1

Likely benign (May 06, 2022) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015)	Pseudohypoaldosteronism, type IB1, autosomal recessive Bronchiectasis with or without elevated sweat chloride 2 Liddle syndrome 3	Fulgent Genetics, Fulgent Genetics Accession: SCV002805337.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022	Observation: 1 Collection method: clinical testing Allele origin: unknown Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: unknown Affected status: unknown

Comment:

The p.Arg577Arg variant in SCNN1A is classified as likely benign because it does not alter an amino acid residue, it is not located within the splice consensus sequence, and splice prediction algorithms do not predict a newly created splice site. It has been identified in 6/24000 African chromosomes by the Genome Aggre gation Database (gnomAD, http://gnomad.broadinstitute.org). ACMG/AMP Criteria ap plied: BP4, BP7.

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs570566104 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 17, 2025