Variant 15-41811358-C-T 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_014994.3(MAPKBP1):c.327+123C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 1,030,254 control chromosomes in the GnomAD database, including 1,655 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.039 ( 179 hom., cov: 32)

Exomes 𝑓: 0.054 ( 1476 hom. )

Consequence

MAPKBP1
NM_014994.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.847

Variant links:

Genes affected

MAPKBP1 (HGNC:29536): (mitogen-activated protein kinase binding protein 1) This gene encodes a scaffold protein that regulates the JNK (c-Jun N-terminal kinase) and NOD2 (nucleotide-binding oligomerization domain-containing protein 2) signaling pathways. The encoded protein interacts with another related JNK pathway scaffold protein, WDR62, via a conserved dimerization domain, and enhances JNK signaling. This protein may play a role in bacterial immunity by binding to the NOD2 receptor and negatively regulating downstream antibacterial and pro-inflammatory signaling. Mutations in this gene that impair cellular localization of the encoded protein cause a form of nephronophthisis, an autosomal-recessive kidney disorder, in human patients. [provided by RefSeq, May 2017]

MAPKBP1 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=-0.87).

BP6

Variant 15-41811358-C-T is Benign according to our data. Variant chr15-41811358-C-T is described in ClinVar as [Benign]. Clinvar id is 1297946.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAPKBP1	NM_014994.3 linkuse as main transcript	c.327+123C>T		intron_variant		ENST00000457542.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPKBP1	ENST00000457542.7 linkuse as main transcript	c.327+123C>T		intron_variant		1	NM_014994.3	P4	O60336-6

Frequencies

GnomAD3 genomes

AF:

0.0395

AC:

6011

AN:

152224

Hom.:

179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0103

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.0219

Gnomad ASJ

AF:

0.0204

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0174

Gnomad FIN

AF:

0.0658

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0629

Gnomad OTH

AF:

0.0296

GnomAD4 exome

AF:

0.0542

AC:

47581

AN:

877912

Hom.:

1476

Cov.:

AF XY:

0.0526

AC XY:

23944

AN XY:

455122

show subpopulations

Gnomad4 AFR exome

AF:

0.00928

Gnomad4 AMR exome

AF:

0.0190

Gnomad4 ASJ exome

AF:

0.0200

Gnomad4 EAS exome

AF:

0.000113

Gnomad4 SAS exome

AF:

0.0230

Gnomad4 FIN exome

AF:

0.0728

Gnomad4 NFE exome

AF:

0.0655

Gnomad4 OTH exome

AF:

0.0457

GnomAD4 genome

AF:

0.0394

AC:

6007

AN:

152342

Hom.:

179

Cov.:

AF XY:

0.0377

AC XY:

2811

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.0103

Gnomad4 AMR

AF:

0.0218

Gnomad4 ASJ

AF:

0.0204

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0170

Gnomad4 FIN

AF:

0.0658

Gnomad4 NFE

AF:

0.0629

Gnomad4 OTH

AF:

0.0293

Alfa

AF:

0.0552

Hom.:

Bravo

AF:

0.0349

Asia WGS

AF:

0.00722

AC:

AN:

3478

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 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.3

DANN

Benign

0.57

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