Variant chr16-1706378-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001318852.2(MAPK8IP3):c.39G>A(p.Val13Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00676 in 1,610,328 control chromosomes in the GnomAD database, including 329 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0043 ( 14 hom., cov: 32)

Exomes 𝑓: 0.0070 ( 315 hom. )

Consequence

MAPK8IP3
NM_001318852.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.49

Variant links:

Genes affected

MAPK8IP3 (HGNC:6884): (mitogen-activated protein kinase 8 interacting protein 3) The protein encoded by this gene shares similarity with the product of Drosophila syd gene, required for the functional interaction of kinesin I with axonal cargo. Studies of the similar gene in mouse suggested that this protein may interact with, and regulate the activity of numerous protein kinases of the JNK signaling pathway, and thus function as a scaffold protein in neuronal cells. The C. elegans counterpart of this gene is found to regulate synaptic vesicle transport possibly by integrating JNK signaling and kinesin-1 transport. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]

MAPK8IP3 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=-0.59).

BP6

Variant 16-1706378-G-A is Benign according to our data. Variant chr16-1706378-G-A is described in ClinVar as [Benign]. Clinvar id is 3039422.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=1.49 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAPK8IP3	NM_001318852.2 link	c.39G>A	p.Val13Val	synonymous_variant	Exon 1 of 32	ENST00000610761.2	NP_001305781.1	Q9UPT6A0A087WYG2B7ZMF3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAPK8IP3	ENST00000610761.2 link	c.39G>A	p.Val13Val	synonymous_variant	Exon 1 of 32	1	NM_001318852.2	ENSP00000481780.1		A0A087WYG2

Frequencies

GnomAD3 genomes

AF:

0.00430

AC:

654

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000965

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00294

Gnomad ASJ

AF:

0.00547

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0786

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00231

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.0116

AC:

2800

AN:

240906

Hom.:

108

AF XY:

0.0153

AC XY:

2006

AN XY:

131384

show subpopulations

Gnomad AFR exome

AF:

0.00107

Gnomad AMR exome

AF:

0.00171

Gnomad ASJ exome

AF:

0.00467

Gnomad EAS exome

AF:

0.00119

Gnomad SAS exome

AF:

0.0813

Gnomad FIN exome

AF:

0.000148

Gnomad NFE exome

AF:

0.00175

Gnomad OTH exome

AF:

0.00632

GnomAD4 exome

AF:

0.00701

AC:

10226

AN:

1458016

Hom.:

315

Cov.:

AF XY:

0.00926

AC XY:

6715

AN XY:

725102

show subpopulations

Gnomad4 AFR exome

AF:

0.000510

Gnomad4 AMR exome

AF:

0.00182

Gnomad4 ASJ exome

AF:

0.00392

Gnomad4 EAS exome

AF:

0.000633

Gnomad4 SAS exome

AF:

0.0791

Gnomad4 FIN exome

AF:

0.0000956

Gnomad4 NFE exome

AF:

0.00250

Gnomad4 OTH exome

AF:

0.00719

GnomAD4 genome

AF:

0.00431

AC:

657

AN:

152312

Hom.:

Cov.:

AF XY:

0.00567

AC XY:

422

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.000962

Gnomad4 AMR

AF:

0.00294

Gnomad4 ASJ

AF:

0.00547

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0791

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.00231

Gnomad4 OTH

AF:

0.00379

Alfa

AF:

0.00226

Hom.:

Bravo

AF:

0.00204

Asia WGS

AF:

0.0440

AC:

152

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MAPK8IP3-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 02, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.90

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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