NM_001927.4(DES):c.559C>T (p.Leu187=) AND not specified

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jan 17, 2022
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:: RCV001823771.1

Allele description [Variation Report for NM_001927.4(DES):c.559C>T (p.Leu187=)]

NM_001927.4(DES):c.559C>T (p.Leu187=)

Gene:

DES:desmin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_001927.4(DES):c.559C>T (p.Leu187=)

HGVS:

NC_000002.12:g.219419021C>T
NG_008043.1:g.5645C>T
NM_001382708.1:c.559C>T
NM_001382709.1:c.559C>T
NM_001382710.1:c.559C>T
NM_001382711.1:c.559C>T
NM_001382712.1:c.559C>T
NM_001382713.1:c.495+64C>T
NM_001927.3:c.559C>T
NM_001927.4:c.559C>TMANE SELECT
NP_001369637.1:p.Leu187=
NP_001369638.1:p.Leu187=
NP_001369639.1:p.Leu187=
NP_001369640.1:p.Leu187=
NP_001369641.1:p.Leu187=
NP_001918.3:p.Leu187=
LRG_380t1:c.559C>T
LRG_380:g.5645C>T
NC_000002.11:g.220283743C>T

Links:

dbSNP: rs1314756792

NCBI 1000 Genomes Browser:

rs1314756792

Molecular consequence:

NM_001382713.1:c.495+64C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001382708.1:c.559C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001382709.1:c.559C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001382710.1:c.559C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001382711.1:c.559C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001382712.1:c.559C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001927.4:c.559C>T - 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
SCV002073443	Phosphorus, Inc.	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jan 17, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002073443

Phosphorus, Inc.

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jan 17, 2022)

germline

clinical testing

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

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Phosphorus, Inc., SCV002073443.1

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

Description

This synonymous variant has an entry in ClinVar (1088216) NM_001927.4 (DES): c.559C>T (p.Leu187=) and has occurred in GnomAD with a total MAF of 0.0015%. This position is conserved. In silico splicing algorithm was unavailable, however it is not predicted to impact splicing due to its distance from the splice site. No functional studies were performed to confirm this prediction. The variant has not occurred in literature associated with disease. Considering the above evidence, this variant has been 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

ClinVar

Relating variation to medicine