VCV000094125.14 - ClinVar

NM_003289.4(TPM2):c.773-4_773-3dup

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(5)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Benign/Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_003289.4(TPM2):c.773-4_773-3dup

Variation ID: 94125 Accession: VCV000094125.14

Type and length

Duplication, 2 bp

Location

Cytogenetic: 9p13.3 9: 35683243-35683244 (GRCh38) [ NCBI UCSC ] 9: 35683240-35683241 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Mar 24, 2015	Feb 20, 2024	Jan 29, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_003289.4:c.773-4_773-3dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_001301226.2:c.772+1001_772+1002dup		intron variant
NM_001301227.2:c.773-4_773-3dup		intron variant
NM_003289.3:c.773-4_773-3dupCC
NM_213674.1:c.772+1001_772+1002dup		intron variant
NC_000009.12:g.35683250_35683251dup
NC_000009.11:g.35683247_35683248dup
NG_011620.1:g.11813_11814dup
LRG_680:g.11813_11814dup
LRG_680t1:c.772+1001_772+1002dup
LRG_680t2:c.773-4_773-3dup

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000009.12:35683243:GGGGGGGG:GGGGGGGGGG

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.26218 (GGGGGGGGG)

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA147644 dbSNP: rs35401252 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
TPM2		-	-	GRCh38 GRCh37	310	388

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not specified	Benign (3)	criteria provided, multiple submitters, no conflicts	Mar 21, 2016	RCV000080088.12
Arthrogryposis, distal, type 1A	Benign (1)	criteria provided, single submitter	Jan 29, 2024	RCV000527724.9
Arthrogryposis, distal, type 1A Congenital myopathy 23 Congenital myopathy with fiber type disproportion	Likely benign (1)	criteria provided, single submitter	Mar 28, 2022	RCV002498408.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	NOT SPECIFIED Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV000309563.1 First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016
Likely benign (Mar 28, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Arthrogryposis, distal, type 1A Congenital myopathy 4A, autosomal dominant Congenital myopathy 23 Affected status: unknown Allele origin: unknown	Fulgent Genetics, Fulgent Genetics Accession: SCV002804531.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022
Benign (Jan 29, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Arthrogryposis, distal, type 1A Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000630178.6 First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024
Benign (Mar 21, 2016)	criteria provided, single submitter (GeneDx Variant Classification (06012015)) Method: clinical testing	not specified Affected status: yes Allele origin: germline	GeneDx Accession: SCV000729989.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018	Comment: 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 … (more) 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. (less)
Benign (Jul 24, 2013)	no assertion criteria provided Method: clinical testing	AllHighlyPenetrant Affected status: unknown Allele origin: germline	Eurofins Ntd Llc (ga) Accession: SCV000111983.3 First in ClinVar: Jan 17, 2014 Last updated: Mar 24, 2015	Publications: PubMed (1) PubMed: 23757202 Observation 1: Number of individuals with the variant: 1 Zygosity: Homozygote, Single Heterozygote Sex: mixed Method: http://genetics.emory.edu/egl/tests/view.php?testid=922 Observation 2: Zygosity: Homozygote, Single Heterozygote Sex: mixed Observation 3: Number of individuals with the variant: 3 Zygosity: Homozygote, Single Heterozygote Sex: mixed Observation 4: Zygosity: Homozygote, Single Heterozygote Sex: mixed

Comment:

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.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs35401252 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jan 13, 2025

ClinVar Genomic variation as it relates to human health

NM_003289.4(TPM2):c.773-4_773-3dup

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs35401252 ...