Variant chr19-7910773-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_145185.4(MAP2K7):c.645C>A(p.Pro215=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00578 in 1,610,106 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. P215P) has been classified as Benign.

Frequency

Genomes: 𝑓 0.0034 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0060 ( 41 hom. )

Consequence

MAP2K7
NM_145185.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.80

Variant links:

Genes affected

MAP2K7 (HGNC:6847): (mitogen-activated protein kinase kinase 7) The protein encoded by this gene is a dual specificity protein kinase that belongs to the MAP kinase kinase family. This kinase specifically activates MAPK8/JNK1 and MAPK9/JNK2, and this kinase itself is phosphorylated and activated by MAP kinase kinase kinases including MAP3K1/MEKK1, MAP3K2/MEKK2,MAP3K3/MEKK5, and MAP4K2/GCK. This kinase is involved in the signal transduction mediating the cell responses to proinflammatory cytokines, and environmental stresses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

MAP2K7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 19-7910773-C-A is Benign according to our data. Variant chr19-7910773-C-A is described in ClinVar as [Benign]. Clinvar id is 710280.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-3.8 with no splicing effect.

BS2

High AC in GnomAd4 at 511 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
MAP2K7	NM_145185.4 linkuse as main transcript	c.645C>A	p.Pro215=	synonymous_variant	6/11	ENST00000397979.4
MAP2K7	NM_001297555.2 linkuse as main transcript	c.693C>A	p.Pro231=	synonymous_variant	7/12
MAP2K7	NM_001297556.2 linkuse as main transcript	c.645C>A	p.Pro215=	synonymous_variant	6/11
MAP2K7	XM_006722800.3 linkuse as main transcript	c.693C>A	p.Pro231=	synonymous_variant	7/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP2K7	ENST00000397979.4 linkuse as main transcript	c.645C>A	p.Pro215=	synonymous_variant	6/11	1	NM_145185.4	P4	O14733-1

Frequencies

GnomAD3 genomes

AF:

0.00339

AC:

514

AN:

151720

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00155

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00262

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000204

Gnomad SAS

AF:

0.00499

Gnomad FIN

AF:

0.000565

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00540

Gnomad OTH

AF:

0.00383

GnomAD3 exomes

AF:

0.00407

AC:

983

AN:

241312

Hom.:

AF XY:

0.00425

AC XY:

562

AN XY:

132280

show subpopulations

Gnomad AFR exome

AF:

0.00132

Gnomad AMR exome

AF:

0.00366

Gnomad ASJ exome

AF:

0.00101

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00456

Gnomad FIN exome

AF:

0.000575

Gnomad NFE exome

AF:

0.00595

Gnomad OTH exome

AF:

0.00593

GnomAD4 exome

AF:

0.00603

AC:

8792

AN:

1458274

Hom.:

Cov.:

AF XY:

0.00602

AC XY:

4365

AN XY:

725408

show subpopulations

Gnomad4 AFR exome

AF:

0.00108

Gnomad4 AMR exome

AF:

0.00346

Gnomad4 ASJ exome

AF:

0.000958

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00454

Gnomad4 FIN exome

AF:

0.00105

Gnomad4 NFE exome

AF:

0.00700

Gnomad4 OTH exome

AF:

0.00571

GnomAD4 genome

AF:

0.00337

AC:

511

AN:

151832

Hom.:

Cov.:

AF XY:

0.00276

AC XY:

205

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.00154

Gnomad4 AMR

AF:

0.00261

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.000205

Gnomad4 SAS

AF:

0.00457

Gnomad4 FIN

AF:

0.000565

Gnomad4 NFE

AF:

0.00538

Gnomad4 OTH

AF:

0.00379

Alfa

AF:

0.00479

Hom.:

Bravo

AF:

0.00354

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

0.060

DANN

Benign

0.73

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over