Variant 8-143717733-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_139021.3(MAPK15):c.106G>A(p.Gly36Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00452 in 1,612,078 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0047 ( 25 hom. )

Consequence

MAPK15
NM_139021.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.27

Variant links:

Genes affected

MAPK15 (HGNC:24667): (mitogen-activated protein kinase 15) Enables MAP kinase activity and chromatin binding activity. Involved in several processes, including dopamine uptake; positive regulation of DNA metabolic process; and regulation of organelle organization. Located in several cellular components, including Golgi apparatus; autophagosome; and microtubule organizing center. Biomarker of breast cancer. [provided by Alliance of Genome Resources, Apr 2022]

MAPK15 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.012811065).

BP6

Variant 8-143717733-G-A is Benign according to our data. Variant chr8-143717733-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2658905.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAPK15	NM_139021.3 linkuse as main transcript	c.106G>A	p.Gly36Ser	missense_variant	2/14	ENST00000338033.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPK15	ENST00000338033.9 linkuse as main transcript	c.106G>A	p.Gly36Ser	missense_variant	2/14	1	NM_139021.3	P1	Q8TD08-1

Frequencies

GnomAD3 genomes

AF:

0.00313

AC:

477

AN:

152200

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000772

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.00288

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00160

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00538

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00286

AC:

704

AN:

245794

Hom.:

AF XY:

0.00278

AC XY:

369

AN XY:

132844

show subpopulations

Gnomad AFR exome

AF:

0.00140

Gnomad AMR exome

AF:

0.00218

Gnomad ASJ exome

AF:

0.000101

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000537

Gnomad FIN exome

AF:

0.00153

Gnomad NFE exome

AF:

0.00490

Gnomad OTH exome

AF:

0.00234

GnomAD4 exome

AF:

0.00466

AC:

6803

AN:

1459760

Hom.:

Cov.:

AF XY:

0.00439

AC XY:

3189

AN XY:

725862

show subpopulations

Gnomad4 AFR exome

AF:

0.000717

Gnomad4 AMR exome

AF:

0.00243

Gnomad4 ASJ exome

AF:

0.0000768

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000701

Gnomad4 FIN exome

AF:

0.00160

Gnomad4 NFE exome

AF:

0.00563

Gnomad4 OTH exome

AF:

0.00439

GnomAD4 genome

AF:

0.00313

AC:

477

AN:

152318

Hom.:

Cov.:

AF XY:

0.00265

AC XY:

197

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.000770

Gnomad4 AMR

AF:

0.00281

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00160

Gnomad4 NFE

AF:

0.00538

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00485

Hom.:

Bravo

AF:

0.00294

TwinsUK

AF:

0.00566

AC:

ALSPAC

AF:

0.00649

AC:

ESP6500AA

AF:

0.00272

AC:

ESP6500EA

AF:

0.00453

AC:

ExAC

AF:

0.00267

AC:

324

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

MAPK15: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Benign

-0.11

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.099

T;.;.

Eigen

Uncertain

0.59

Eigen_PC

Uncertain

0.54

FATHMM_MKL

Uncertain

0.93

LIST_S2

Uncertain

0.97

.;D;D

M_CAP

Benign

0.043

MetaRNN

Benign

0.013

T;T;T

MetaSVM

Benign

-0.64

MutationAssessor

Uncertain

2.2

M;M;M

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.55

PROVEAN

Uncertain

-4.2

D;D;D

REVEL

Uncertain

0.37

Sift

Uncertain

0.029

D;T;T

Sift4G

Uncertain

0.057

T;T;T

Polyphen

1.0

D;.;.

Vest4

0.65

MVP

0.85

MPC

0.17

ClinPred

0.017

GERP RS

4.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.37

gMVP

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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