Variant 19-7911231-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_145185.4(MAP2K7):c.856-19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 1,605,132 control chromosomes in the GnomAD database, including 283,355 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.63 ( 30391 hom., cov: 28)

Exomes 𝑓: 0.59 ( 252964 hom. )

Consequence

MAP2K7
NM_145185.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.52

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 19-7911231-T-C is Benign according to our data. Variant chr19-7911231-T-C is described in ClinVar as [Benign]. Clinvar id is 1243653.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
MAP2K7	NM_145185.4 linkuse as main transcript	c.856-19T>C	intron_variant	ENST00000397979.4
MAP2K7	NM_001297555.2 linkuse as main transcript	c.904-19T>C	intron_variant
MAP2K7	NM_001297556.2 linkuse as main transcript	c.856-19T>C	intron_variant
MAP2K7	XM_006722800.3 linkuse as main transcript	c.904-19T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP2K7	ENST00000397979.4 linkuse as main transcript	c.856-19T>C		intron_variant		1	NM_145185.4	P4	O14733-1

Frequencies

GnomAD3 genomes

AF:

0.631

AC:

95376

AN:

151068

Hom.:

30373

Cov.:

show subpopulations

Gnomad AFR

AF:

0.733

Gnomad AMI

AF:

0.687

Gnomad AMR

AF:

0.633

Gnomad ASJ

AF:

0.614

Gnomad EAS

AF:

0.526

Gnomad SAS

AF:

0.712

Gnomad FIN

AF:

0.582

Gnomad MID

AF:

0.577

Gnomad NFE

AF:

0.580

Gnomad OTH

AF:

0.620

GnomAD3 exomes

AF:

0.610

AC:

148109

AN:

242898

Hom.:

45581

AF XY:

0.610

AC XY:

81136

AN XY:

132982

show subpopulations

Gnomad AFR exome

AF:

0.742

Gnomad AMR exome

AF:

0.656

Gnomad ASJ exome

AF:

0.599

Gnomad EAS exome

AF:

0.529

Gnomad SAS exome

AF:

0.704

Gnomad FIN exome

AF:

0.589

Gnomad NFE exome

AF:

0.570

Gnomad OTH exome

AF:

0.601

GnomAD4 exome

AF:

0.588

AC:

855103

AN:

1453948

Hom.:

252964

Cov.:

AF XY:

0.591

AC XY:

427513

AN XY:

723386

show subpopulations

Gnomad4 AFR exome

AF:

0.738

Gnomad4 AMR exome

AF:

0.652

Gnomad4 ASJ exome

AF:

0.602

Gnomad4 EAS exome

AF:

0.497

Gnomad4 SAS exome

AF:

0.706

Gnomad4 FIN exome

AF:

0.580

Gnomad4 NFE exome

AF:

0.575

Gnomad4 OTH exome

AF:

0.590

GnomAD4 genome

AF:

0.631

AC:

95439

AN:

151184

Hom.:

30391

Cov.:

AF XY:

0.632

AC XY:

46700

AN XY:

73848

show subpopulations

Gnomad4 AFR

AF:

0.732

Gnomad4 AMR

AF:

0.633

Gnomad4 ASJ

AF:

0.614

Gnomad4 EAS

AF:

0.525

Gnomad4 SAS

AF:

0.711

Gnomad4 FIN

AF:

0.582

Gnomad4 NFE

AF:

0.580

Gnomad4 OTH

AF:

0.620

Alfa

AF:

0.602

Hom.:

5024

Bravo

AF:

0.636

Asia WGS

AF:

0.634

AC:

2202

AN:

3476

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

GeneDx

May 28, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.4

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

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