NM_152906.7(TANGO2):c.56+122_56+131del AND not specified

Germline classification:: Benign (1 submission)
Last evaluated:: May 3, 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:: RCV002271955.1

Allele description [Variation Report for NM_152906.7(TANGO2):c.56+122_56+131del]

NM_152906.7(TANGO2):c.56+122_56+131del

Gene:

TANGO2:transport and golgi organization 2 homolog [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_152906.7(TANGO2):c.56+122_56+131del

HGVS:

NC_000022.11:g.20036976_20036985del
NG_046857.1:g.24977_24986del
NM_001283106.3:c.56+122_56+131del
NM_001283116.3:c.56+122_56+131del
NM_001283129.3:c.61_70del
NM_001283148.3:c.56+122_56+131del
NM_001283154.3:c.56+122_56+131del
NM_001283179.3:c.56+122_56+131del
NM_001283186.3:c.56+122_56+131del
NM_001283199.3:c.56+122_56+131del
NM_001283215.3:c.61_70del
NM_001283235.3:c.-124+122_-124+131del
NM_001283248.3:c.56+122_56+131del
NM_001322141.2:c.61_70del
NM_001322142.2:c.56+122_56+131del
NM_001322143.2:c.61_70del
NM_001322144.2:c.61_70del
NM_001322145.2:c.61_70del
NM_001322146.2:c.-124+122_-124+131del
NM_001322147.2:c.61_70del
NM_001322148.2:c.-242_-233del
NM_001322149.2:c.61_70del
NM_001322150.2:c.-242_-233del
NM_001322153.2:c.-124+122_-124+131del
NM_001322155.2:c.-124+122_-124+131del
NM_001322160.2:c.-124+122_-124+131del
NM_001322163.2:c.56+122_56+131del
NM_001322166.2:c.56+122_56+131del
NM_001322167.2:c.56+122_56+131del
NM_001322169.2:c.56+122_56+131del
NM_001322171.2:c.-124+122_-124+131del
NM_001322172.2:c.-242_-233del
NM_001322173.2:c.-242_-233del
NM_001322174.2:c.-124+122_-124+131del
NM_001322175.2:c.-124+122_-124+131del
NM_152906.7:c.56+122_56+131delMANE SELECT
NP_001270058.1:p.Trp21fs
NP_001270144.1:p.Trp21fs
NP_001309070.1:p.Trp21fs
NP_001309072.1:p.Trp21fs
NP_001309073.1:p.Trp21fs
NP_001309074.1:p.Trp21fs
NP_001309076.1:p.Trp21fs
NP_001309078.1:p.Trp21fs
NC_000022.10:g.20024499_20024508del
NM_152906.6:c.56+122_56+131del10
NR_104275.3:n.242_251del

Protein change:

W21fs

Links:

dbSNP: rs545147497

NCBI 1000 Genomes Browser:

rs545147497

Molecular consequence:

NM_001322148.2:c.-242_-233del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322150.2:c.-242_-233del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322172.2:c.-242_-233del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322173.2:c.-242_-233del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001283129.3:c.61_70del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001283215.3:c.61_70del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322141.2:c.61_70del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322143.2:c.61_70del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322144.2:c.61_70del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322145.2:c.61_70del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322147.2:c.61_70del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322149.2:c.61_70del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001283106.3:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001283116.3:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001283148.3:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001283154.3:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001283179.3:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001283186.3:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001283199.3:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001283235.3:c.-124+122_-124+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001283248.3:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322142.2:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322146.2:c.-124+122_-124+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322153.2:c.-124+122_-124+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322155.2:c.-124+122_-124+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322160.2:c.-124+122_-124+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322163.2:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322166.2:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322167.2:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322169.2:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322171.2:c.-124+122_-124+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322174.2:c.-124+122_-124+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322175.2:c.-124+122_-124+131del - intron variant - [Sequence Ontology: SO:0001627]
NM_152906.7:c.56+122_56+131del - intron variant - [Sequence Ontology: SO:0001627]
NR_104275.3:n.242_251del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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cytochrome oxidase subunit I, partial (mitochondrion) [Parevania sp. DERV064]
cytochrome oxidase subunit I, partial (mitochondrion) [Parevania sp. DERV064]
gi|60476536|gb|AAX21410.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002556297	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (May 3, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002556297

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(May 3, 2022)

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, SCV002556297.1

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

Description

Variant summary: C22orf25 (aka. TANGO2) c.56+122_56+131del10 is located at a position not widely known to affect splicing. 4/4 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 0.00039 in 277874 control chromosomes, predominantly at a frequency of 0.0052 within the East Asian subpopulation in the gnomAD database, suggesting the variant might be benign. To our knowledge, no occurrence of c.56+122_56+131del10 in individuals affected with Recurrent Metabolic Encephalomyopathic Crises-Rhabdomyolysis Arrhythmia-Intellectual Disability Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as 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: Dec 24, 2023

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