NM_005184.4(CALM3):c.165G>A (p.Glu55=) AND not specified

Germline classification:: Likely benign (1 submission)
Last evaluated:: Nov 7, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003479444.1

Allele description [Variation Report for NM_005184.4(CALM3):c.165G>A (p.Glu55=)]

NM_005184.4(CALM3):c.165G>A (p.Glu55=)

Gene:

CALM3:calmodulin 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.32

Genomic location:

Preferred name:

NM_005184.4(CALM3):c.165G>A (p.Glu55=)

HGVS:

NC_000019.10:g.46608327G>A
NG_051331.1:g.12254G>A
NM_001329921.1:c.57G>A
NM_001329922.1:c.165G>A
NM_001329923.1:c.57G>A
NM_001329924.2:c.57G>A
NM_001329925.2:c.57G>A
NM_001329926.2:c.57G>A
NM_005184.4:c.165G>AMANE SELECT
NP_001316850.1:p.Glu19=
NP_001316851.1:p.Glu55=
NP_001316852.1:p.Glu19=
NP_001316853.1:p.Glu19=
NP_001316854.1:p.Glu19=
NP_001316855.1:p.Glu19=
NP_005175.2:p.Glu55=
LRG_1082t1:c.165G>A
LRG_1082:g.12254G>A
LRG_1082p1:p.Glu55=
NC_000019.9:g.47111584G>A
NM_005184.2:c.165G>A

Molecular consequence:

NM_001329921.1:c.57G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001329922.1:c.165G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001329923.1:c.57G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001329924.2:c.57G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001329925.2:c.57G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001329926.2:c.57G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_005184.4:c.165G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004223463	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Nov 7, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004223463

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(Nov 7, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004223463.1

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

Description

Variant summary: CALM3 c.165G>A alters a conserved nucleotide resulting in a synonymous change. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 2e-05 in 251138 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.165G>A in individuals affected with Long QT Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. A co-occurrence with another pathogenic variant has been observed in our laboratory (FLNC c.1880_1887delATGTGCGG, p.Asp672ValfsX16; internal testing), providing supporting evidence for a benign role. One submitter has reported clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

#	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

Last Updated: Sep 29, 2024

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