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NM_002474.3(MYH11):c.5566C>T (p.Leu1856=) AND not specified

Germline classification:
Benign (2 submissions)
Last evaluated:
May 14, 2018
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000126967.16

Allele description [Variation Report for NM_002474.3(MYH11):c.5566C>T (p.Leu1856=)]

NM_002474.3(MYH11):c.5566C>T (p.Leu1856=)

Genes:
MYH11:myosin heavy chain 11 [Gene - OMIM - HGNC]
NDE1:nudE neurodevelopment protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.11
Genomic location:
Preferred name:
NM_002474.3(MYH11):c.5566C>T (p.Leu1856=)
Other names:
p.L1856L:CTG>TTG
HGVS:
  • NC_000016.10:g.15715211G>A
  • NG_009299.1:g.146820C>T
  • NG_021210.1:g.76945G>A
  • NM_001040113.2:c.5587C>T
  • NM_001040114.2:c.5587C>T
  • NM_001143979.2:c.948-8980G>A
  • NM_002474.3:c.5566C>TMANE SELECT
  • NM_017668.3:c.948-8980G>AMANE SELECT
  • NM_022844.3:c.5566C>T
  • NP_001035202.1:p.Leu1863=
  • NP_001035203.1:p.Leu1863=
  • NP_002465.1:p.Leu1856=
  • NP_074035.1:p.Leu1856=
  • LRG_1401t1:c.5566C>T
  • LRG_1401t2:c.5587C>T
  • LRG_1401:g.146820C>T
  • LRG_1401p1:p.Leu1856=
  • LRG_1401p2:p.Leu1863=
  • NC_000016.9:g.15809068G>A
  • NM_001040113.1:c.5587C>T
  • NM_001143979.1:c.948-8980G>A
  • NM_002474.2:c.5566C>T
Links:
dbSNP: rs142639688
NCBI 1000 Genomes Browser:
rs142639688
Molecular consequence:
  • NM_001143979.2:c.948-8980G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_017668.3:c.948-8980G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001040113.2:c.5587C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001040114.2:c.5587C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_002474.3:c.5566C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_022844.3:c.5566C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000170498GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Benign
(Oct 14, 2013)
germlineclinical testing

Citation Link,

SCV000917828Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Benign
(May 14, 2018)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

First genetic analysis of aneurysm genes in familial and sporadic abdominal aortic aneurysm.

van de Luijtgaarden KM, Heijsman D, Maugeri A, Weiss MM, Verhagen HJ, IJpma A, Br├╝ggenwirth HT, Majoor-Krakauer D.

Hum Genet. 2015 Aug;134(8):881-93. doi: 10.1007/s00439-015-1567-0. Epub 2015 May 28.

PubMed [citation]
PMID:
26017485
PMCID:
PMC4495250

Details of each submission

From GeneDx, SCV000170498.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000917828.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: MYH11 c.5587C>T alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational 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 0.0013 in 277156 control chromosomes in the gnomAD database, including 1 homozygotes. The observed variant frequency is approximately 1048-fold higher than the estimated maximal expected allele frequency for a pathogenic variant in MYH11 causing Aortopathy phenotype (1.3e-06), strongly suggesting that the variant is benign. The variant, c.5587C>T, has been reported in the literature in one individual affected with Aortopathy (van de Luijtgaarden_2015). This report does not provide unequivocal conclusions about association of the variant with Aortopathy. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Multiple ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as "likely benign/benign." Based on the evidence outlined above, the variant was classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 15, 2024