NM_139276.3(STAT3):c.2144+46_2144+47del AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 28, 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:: RCV002223065.1

Allele description [Variation Report for NM_139276.3(STAT3):c.2144+46_2144+47del]

NM_139276.3(STAT3):c.2144+46_2144+47del

Gene:

STAT3:signal transducer and activator of transcription 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q21.2

Genomic location:

Preferred name:

NM_139276.3(STAT3):c.2144+46_2144+47del

HGVS:

NC_000017.11:g.42317135_42317136del
NG_007370.1:g.76360_76361del
NM_001369512.1:c.2144+46_2144+47del
NM_001369513.1:c.2144+46_2144+47del
NM_001369514.1:c.2141+46_2141+47del
NM_001369516.1:c.2141+46_2141+47del
NM_001369517.1:c.2144+46_2144+47del
NM_001369518.1:c.2144+46_2144+47del
NM_001369519.1:c.2141+46_2141+47del
NM_001369520.1:c.2141+46_2141+47del
NM_001384984.1:c.2060+46_2060+47del
NM_001384985.1:c.2066+46_2066+47del
NM_001384986.1:c.2156+46_2156+47del
NM_001384987.1:c.2123+46_2123+47del
NM_001384988.1:c.2099-285_2099-284del
NM_001384989.1:c.2045+46_2045+47del
NM_001384990.1:c.2159+46_2159+47del
NM_001384991.1:c.2117+46_2117+47del
NM_001384992.1:c.2084+46_2084+47del
NM_001384993.1:c.2144+46_2144+47del
NM_003150.4:c.2141+46_2141+47del
NM_139276.3:c.2144+46_2144+47delMANE SELECT
NM_213662.2:c.2144+46_2144+47del
LRG_112t1:c.2144+46_2144+47del
LRG_112:g.76360_76361del
NC_000017.10:g.40469153_40469154del
NM_139276.2:c.2144+46_2144+47delCA

Links:

dbSNP: rs1279773038

NCBI 1000 Genomes Browser:

rs1279773038

Molecular consequence:

NM_001369512.1:c.2144+46_2144+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369513.1:c.2144+46_2144+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369514.1:c.2141+46_2141+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369516.1:c.2141+46_2141+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369517.1:c.2144+46_2144+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369518.1:c.2144+46_2144+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369519.1:c.2141+46_2141+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369520.1:c.2141+46_2141+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384984.1:c.2060+46_2060+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384985.1:c.2066+46_2066+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384986.1:c.2156+46_2156+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384987.1:c.2123+46_2123+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384988.1:c.2099-285_2099-284del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384989.1:c.2045+46_2045+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384990.1:c.2159+46_2159+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384991.1:c.2117+46_2117+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384992.1:c.2084+46_2084+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384993.1:c.2144+46_2144+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_003150.4:c.2141+46_2141+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_139276.3:c.2144+46_2144+47del - intron variant - [Sequence Ontology: SO:0001627]
NM_213662.2:c.2144+46_2144+47del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Bakawan sp. 1 TRO-2019 voucher MNHN 42265 histone H3 (H3) gene, partial cds
Bakawan sp. 1 TRO-2019 voucher MNHN 42265 histone H3 (H3) gene, partial cds
gi|1798058532|gb|MH933477.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002500725	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Mar 28, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002500725

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Mar 28, 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, SCV002500725.1

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

Description

Variant summary: STAT3 c.2144+46_2144+47delCA is located at a position not widely known to affect splicing. Four computational tools predict the variant abolishes a cryptic intronic 3' acceptor site but does not affect any canonical splice sites. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 250252 control chromosomes (gnomAD v2.1.1). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.2144+46_2144+47delCA in individuals affected with Autoimmune Disease, Multisystem, Infantile-Onset, 1 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 uncertain significance.

#	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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