NM_052867.4(NALCN):c.3852C>A (p.Gly1284=) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Dec 31, 2023
Review status:: criteria provided, conflicting classifications

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000877305.12

Allele description [Variation Report for NM_052867.4(NALCN):c.3852C>A (p.Gly1284=)]

NM_052867.4(NALCN):c.3852C>A (p.Gly1284=)

Gene:

NALCN:sodium leak channel, non-selective [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q32.3

Genomic location:

Preferred name:

NM_052867.4(NALCN):c.3852C>A (p.Gly1284=)

HGVS:

NC_000013.11:g.101081560G>T
NG_053176.1:g.340647C>A
NM_001350748.2:c.3939C>A
NM_001350749.2:c.3852C>A
NM_001350750.2:c.3765C>A
NM_001350751.2:c.3765C>A
NM_052867.4:c.3852C>AMANE SELECT
NP_001337677.1:p.Gly1313=
NP_001337678.1:p.Gly1284=
NP_001337679.1:p.Gly1255=
NP_001337680.1:p.Gly1255=
NP_443099.1:p.Gly1284=
NC_000013.10:g.101733911G>T
NC_000013.10:g.101733911G>T
NM_052867.2:c.3852C>A

Links:

dbSNP: rs772803115

NCBI 1000 Genomes Browser:

rs772803115

Molecular consequence:

NM_001350748.2:c.3939C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001350749.2:c.3852C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001350750.2:c.3765C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001350751.2:c.3765C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_052867.4:c.3852C>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Dikarya 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1,...
Dikarya 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence.
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001020023	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 31, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001790988	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Nov 22, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001020023

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 31, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001790988

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Nov 22, 2021)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001020023.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV001790988.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

In-silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Has not been previously published as pathogenic or benign to our knowledge

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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