NM_001111125.3(IQSEC2):c.999+4C>T AND not provided

Germline classification:: Benign (1 submission)
Last evaluated:: Jul 2, 2020
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:: RCV001714077.2

Allele description [Variation Report for NM_001111125.3(IQSEC2):c.999+4C>T]

NM_001111125.3(IQSEC2):c.999+4C>T

Gene:

IQSEC2:IQ motif and Sec7 domain ArfGEF 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.22

Genomic location:

Preferred name:

NM_001111125.3(IQSEC2):c.999+4C>T

HGVS:

NC_000023.11:g.53255796G>A
NG_021296.2:g.70555C>T
NM_001111125.3:c.999+4C>TMANE SELECT
NM_015075.2:c.384+4C>T
LRG_1194t1:c.999+4C>T
LRG_1194:g.70555C>T
NC_000023.10:g.53284978G>A

Links:

dbSNP: rs199648681

NCBI 1000 Genomes Browser:

rs199648681

Molecular consequence:

NM_001111125.3:c.999+4C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_015075.2:c.384+4C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001941185	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Jul 2, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001941185

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Jul 2, 2020)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV001941185.2

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

Description

Has not been previously published as pathogenic or benign to our knowledge; In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Observed in 0.0162% (33/203140 alleles) in large population cohorts (Lek et al., 2016)

#	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: Dec 24, 2023

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