chr19-4101009-G-A

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.705+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000257 in 1,554,168 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 0.000046 ( 0 hom., cov: 30)

Exomes 𝑓: 0.000024 ( 0 hom. )

Consequence

MAP2K2
NM_030662.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.299

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=-0.88).

BP6

Variant 19-4101009-G-A is Benign according to our data. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-4101009-G-A is described in CliVar as Likely_benign. Clinvar id is 46241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 7 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MAP2K2	NM_030662.4 link	c.705+10C>T	intron_variant	Intron 6 of 10	ENST00000262948.10	NP_109587.1	P36507
MAP2K2	NM_001440688.1 link	c.705+10C>T	intron_variant	Intron 6 of 8		NP_001427617.1
MAP2K2	NM_001440689.1 link	c.135+10C>T	intron_variant	Intron 4 of 8		NP_001427618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP2K2	ENST00000262948.10 link	c.705+10C>T		intron_variant	Intron 6 of 10	1	NM_030662.4	ENSP00000262948.4		P36507

Frequencies

GnomAD3 genomes

AF:

0.0000460

AC:

AN:

152034

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000967

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000441

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000184

AC:

AN:

162878

AF XY:

0.0000116

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000465

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000235

AC:

AN:

1402134

Hom.:

Cov.:

AF XY:

0.0000217

AC XY:

AN XY:

692052

show subpopulations

African (AFR)

AF:

0.0000315

AC:

AN:

31754

American (AMR)

AF:

0.00

AC:

AN:

35970

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25222

East Asian (EAS)

AF:

0.00

AC:

AN:

36142

South Asian (SAS)

AF:

0.00

AC:

AN:

79558

European-Finnish (FIN)

AF:

0.00

AC:

AN:

49558

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4212

European-Non Finnish (NFE)

AF:

0.0000296

AC:

AN:

1081594

Other (OTH)

AF:

0.00

AC:

AN:

58124

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

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:

0.0000460

AC:

AN:

152034

Hom.:

Cov.:

AF XY:

0.0000404

AC XY:

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.0000967

AC:

AN:

41386

American (AMR)

AF:

0.00

AC:

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5170

South Asian (SAS)

AF:

0.00

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000441

AC:

AN:

67988

Other (OTH)

AF:

0.00

AC:

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

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:

0.000102

Hom.:

Bravo

AF:

0.0000642

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Dec 09, 2008

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Oct 06, 2016

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

RASopathy

Benign:1

Jul 16, 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

-0.88

CADD

Benign

7.0

(source)

DANN

Benign

0.59

PhyloP100

0.30

PromoterAI

-0.018

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

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