chr19-4110496-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_030662.4(MAP2K2):c.450+13G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,636 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000014 ( 0 hom. )

Consequence

MAP2K2
NM_030662.4 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.33

Publications

0 publications found

Variant links:

Genes affected

MAP2K2 (HGNC:6842): (mitogen-activated protein kinase kinase 2) The protein encoded by this gene is a dual specificity protein kinase that belongs to the MAP kinase kinase family. This kinase is known to play a critical role in mitogen growth factor signal transduction. It phosphorylates and thus activates MAPK1/ERK2 and MAPK2/ERK3. The activation of this kinase itself is dependent on the Ser/Thr phosphorylation by MAP kinase kinase kinases. Mutations in this gene cause cardiofaciocutaneous syndrome (CFC syndrome), a disease characterized by heart defects, cognitive disability, and distinctive facial features similar to those found in Noonan syndrome. The inhibition or degradation of this kinase is also found to be involved in the pathogenesis of Yersinia and anthrax. A pseudogene, which is located on chromosome 7, has been identified for this gene. [provided by RefSeq, Jul 2008]

MAP2K2 Gene-Disease associations (from GenCC):

cardiofaciocutaneous syndrome
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
cardiofaciocutaneous syndrome 4
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, PanelApp Australia, Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
neurofibromatosis-Noonan syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Noonan syndrome
Inheritance: AD Classification: LIMITED Submitted by: ClinGen

MAP2K2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 19-4110496-C-T is Benign according to our data. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4110496-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 178864.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP2K2	NM_030662.4 link	c.450+13G>A		intron_variant	Intron 3 of 10	ENST00000262948.10	NP_109587.1	P36507
MAP2K2	NM_001440688.1 link	c.450+13G>A		intron_variant	Intron 3 of 8		NP_001427617.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MAP2K2	ENST00000262948.10 link	c.450+13G>A	intron_variant	Intron 3 of 10	1	NM_030662.4	ENSP00000262948.4	P36507
MAP2K2	ENST00000394867.9 link	n.889+13G>A	intron_variant	Intron 2 of 9	5
MAP2K2	ENST00000599345.1 link	n.647+13G>A	intron_variant	Intron 3 of 6	5
MAP2K2	ENST00000687128.1 link	n.889+13G>A	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.0000394

AC:

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000655

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000440

AC:

AN:

249932

AF XY:

0.0000296

show subpopulations

Gnomad AFR exome

AF:

0.000123

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000272

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000882

Gnomad OTH exome

AF:

0.000164

GnomAD4 exome

AF:

0.0000144

AC:

AN:

1460342

Hom.:

Cov.:

AF XY:

0.0000138

AC XY:

AN XY:

726496

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33480

American (AMR)

AF:

0.00

AC:

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26132

East Asian (EAS)

AF:

0.000176

AC:

AN:

39700

South Asian (SAS)

AF:

0.0000696

AC:

AN:

86254

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51936

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00000450

AC:

AN:

1111970

Other (OTH)

AF:

0.0000497

AC:

AN:

60380

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000394

AC:

AN:

152294

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.0000481

AC:

AN:

41558

American (AMR)

AF:

0.0000654

AC:

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.000386

AC:

AN:

5184

South Asian (SAS)

AF:

0.000207

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68022

Other (OTH)

AF:

0.00

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.433

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000453

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Mar 27, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

450+13G>A in intron 3 of MAP2K2: This variant is not expected to have clinical significance as it does not alter a coding or splice consensus sequence. -

Dec 10, 2023

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

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

RASopathy

Benign:1

Oct 15, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.099

(source)

DANN

Benign

0.61

PhyloP100

-1.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over