NM_030662.4(MAP2K2):c.1093-6T>C AND not provided

Germline classification:: Benign (2 submissions)
Last evaluated:: Dec 18, 2019
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:: RCV000590120.5

Allele description [Variation Report for NM_030662.4(MAP2K2):c.1093-6T>C]

NM_030662.4(MAP2K2):c.1093-6T>C

Gene:

MAP2K2:mitogen-activated protein kinase kinase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.3

Genomic location:

Preferred name:

NM_030662.4(MAP2K2):c.1093-6T>C

HGVS:

NC_000019.10:g.4090714A>G
NG_007996.1:g.38415T>C
NM_030662.4:c.1093-6T>CMANE SELECT
LRG_750t1:c.1093-6T>C
LRG_750:g.38415T>C
NC_000019.9:g.4090712A>G
NM_030662.3:c.1093-6T>C
c.1093-6T>C

Links:

dbSNP: rs369681843

NCBI 1000 Genomes Browser:

rs369681843

Molecular consequence:

NM_030662.4:c.1093-6T>C - 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
SCV000513532	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Dec 18, 2019)	germline	clinical testing	Citation Link,
SCV000699627	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Aug 15, 2016)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000513532

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Dec 18, 2019)

germline

clinical testing

Citation Link,

SCV000699627

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Aug 15, 2016)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx

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

Details of each submission

From GeneDx, SCV000513532.6

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

#	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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699627.1

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

Description

Variant summary: The MAP2K2 c.1093-6T>C variant involves the alteration of a conserved intronic nucleotide. Mutation Taster predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 9/21250 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.0031757 (9/2834). This frequency is about 1270 times the estimated maximal expected allele frequency of a pathogenic MAP2K2 variant (0.0000025), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. One clinical diagnostic laboratory has classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant is 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: Sep 29, 2024

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