NM_002470.4(MYH3):c.1960-8del AND Contractures, pterygia, and variable skeletal fusions syndrome 1B

Germline classification:: Benign (2 submissions)
Last evaluated:: May 4, 2023
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:: RCV001778906.3

Allele description [Variation Report for NM_002470.4(MYH3):c.1960-8del]

NM_002470.4(MYH3):c.1960-8del

Gene:

MYH3:myosin heavy chain 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_002470.4(MYH3):c.1960-8del

HGVS:

NC_000017.11:g.10641389del
NG_011537.1:g.20919del
NM_002470.4:c.1960-8delMANE SELECT
NC_000017.10:g.10544697del
NC_000017.10:g.10544706del
NM_002470.3:c.1960-8delT
NM_002470.4:c.1960-8delTMANE SELECT

Links:

dbSNP: rs3216884

NCBI 1000 Genomes Browser:

rs3216884

Molecular consequence:

NM_002470.4:c.1960-8del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Contractures, pterygia, and variable skeletal fusions syndrome 1B
Synonyms:: CONTRACTURES, PTERYGIA, AND SPONDYLOCARPOTARSAL FUSION SYNDROME 1B
Identifiers:: MONDO: MONDO:0020746; MedGen: C5193114; OMIM: 618469

Recent activity

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lysine ketoglutarate reductase trans-splicing protein (DUF707) [Arabidopsis thal...
lysine ketoglutarate reductase trans-splicing protein (DUF707) [Arabidopsis thaliana]
gi|22331371|ref|NP_189383.2|

Protein
PLCD1 [Protobothrops mucrosquamatus]
PLCD1 [Protobothrops mucrosquamatus]
Gene ID:107284364

Gene
pol [African green monkey simian foamy virus]
pol [African green monkey simian foamy virus]
Gene ID:6386654

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002016125	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Sep 5, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004812820	Molecular Genetics, Royal Melbourne Hospital See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (May 4, 2023)	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

SCV002016125

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Sep 5, 2021)

germline

clinical testing

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

SCV004812820

Molecular Genetics, Royal Melbourne Hospital

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(May 4, 2023)

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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	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 Genome-Nilou Lab, SCV002016125.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Molecular Genetics, Royal Melbourne Hospital, SCV004812820.1

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

Description

European Non-Finnish population allele frequency is 73.31% (rs767372373, 93,270/126,364 alleles, 33,886 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.1.0, this variant is classified as BENIGN. Following criteria are met: BA1

#	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: Apr 20, 2024

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