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NM_030662.4(MAP2K2):c.919+4C>T AND not specified

Germline classification:
Benign (1 submission)
Last evaluated:
Nov 2, 2021
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:
RCV001797594.9

Allele description [Variation Report for NM_030662.4(MAP2K2):c.919+4C>T]

NM_030662.4(MAP2K2):c.919+4C>T

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.919+4C>T
HGVS:
  • NC_000019.10:g.4099197G>A
  • NG_007996.1:g.29932C>T
  • NM_030662.4:c.919+4C>TMANE SELECT
  • LRG_750t1:c.919+4C>T
  • LRG_750:g.29932C>T
  • NC_000019.9:g.4099195G>A
  • NC_000019.9:g.4099195G>A
  • NM_030662.3(MAP2K2):c.919+4C>T
  • NM_030662.3:c.919+4C>T
Links:
dbSNP: rs763424788
NCBI 1000 Genomes Browser:
rs763424788
Molecular consequence:
  • NM_030662.4:c.919+4C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000699649Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Nov 2, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699649.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: MAP2K2 c.919+4C>T alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 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 4.4e-05 in 248150 control chromosomes. The observed variant frequency is approximately 18 fold of the estimated maximal expected allele frequency for a pathogenic variant in MAP2K2 causing Noonan Syndrome And Related Conditions phenotype (2.5e-06), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.919+4C>T in individuals affected with Noonan Syndrome And Related Conditions and no experimental evidence demonstrating its impact on protein function have been reported. Three ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (n=1) and likely benign (n=2). Based on the evidence outlined above, the variant was classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024