Variant rs1129156 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002446.4(MAP3K10):c.1818T>C(p.Phe606=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 1,582,998 control chromosomes in the GnomAD database, including 428,731 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.75 ( 43064 hom., cov: 33)

Exomes 𝑓: 0.73 ( 385667 hom. )

Consequence

MAP3K10
NM_002446.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.279

Variant links:

Genes affected

MAP3K10 (HGNC:6849): (mitogen-activated protein kinase kinase kinase 10) The protein encoded by this gene is a member of the serine/threonine kinase family. This kinase has been shown to activate MAPK8/JNK and MKK4/SEK1, and this kinase itself can be phoshorylated, and thus activated by JNK kinases. This kinase functions preferentially on the JNK signaling pathway, and is reported to be involved in nerve growth factor (NGF) induced neuronal apoptosis. [provided by RefSeq, Jul 2008]

MAP3K10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP7

Synonymous conserved (PhyloP=-0.279 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP3K10	NM_002446.4 linkuse as main transcript	c.1818T>C	p.Phe606=	synonymous_variant	8/10	ENST00000253055.8	NP_002437.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
MAP3K10	ENST00000253055.8 linkuse as main transcript	c.1818T>C	p.Phe606=	synonymous_variant	8/10	1	NM_002446.4	ENSP00000253055	P1
MAP3K10	ENST00000594791.1 linkuse as main transcript	n.334T>C		non_coding_transcript_exon_variant	3/3	3
MAP3K10	ENST00000593502.5 linkuse as main transcript	c.*278T>C		3_prime_UTR_variant, NMD_transcript_variant	5/5	3		ENSP00000473021
MAP3K10	ENST00000597986.5 linkuse as main transcript	c.*278T>C		3_prime_UTR_variant, NMD_transcript_variant	6/8	5		ENSP00000471916

Frequencies

GnomAD3 genomes

AF:

0.751

AC:

114089

AN:

152016

Hom.:

43030

Cov.:

show subpopulations

Gnomad AFR

AF:

0.807

Gnomad AMI

AF:

0.808

Gnomad AMR

AF:

0.764

Gnomad ASJ

AF:

0.643

Gnomad EAS

AF:

0.693

Gnomad SAS

AF:

0.777

Gnomad FIN

AF:

0.696

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.729

Gnomad OTH

AF:

0.742

GnomAD3 exomes

AF:

0.733

AC:

147839

AN:

201660

Hom.:

54208

AF XY:

0.732

AC XY:

78934

AN XY:

107768

show subpopulations

Gnomad AFR exome

AF:

0.804

Gnomad AMR exome

AF:

0.767

Gnomad ASJ exome

AF:

0.633

Gnomad EAS exome

AF:

0.698

Gnomad SAS exome

AF:

0.772

Gnomad FIN exome

AF:

0.696

Gnomad NFE exome

AF:

0.725

Gnomad OTH exome

AF:

0.727

GnomAD4 exome

AF:

0.734

AC:

1049765

AN:

1430864

Hom.:

385667

Cov.:

AF XY:

0.734

AC XY:

519942

AN XY:

708630

show subpopulations

Gnomad4 AFR exome

AF:

0.806

Gnomad4 AMR exome

AF:

0.764

Gnomad4 ASJ exome

AF:

0.633

Gnomad4 EAS exome

AF:

0.683

Gnomad4 SAS exome

AF:

0.772

Gnomad4 FIN exome

AF:

0.700

Gnomad4 NFE exome

AF:

0.733

Gnomad4 OTH exome

AF:

0.737

GnomAD4 genome

AF:

0.751

AC:

114188

AN:

152134

Hom.:

43064

Cov.:

AF XY:

0.748

AC XY:

55594

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.807

Gnomad4 AMR

AF:

0.764

Gnomad4 ASJ

AF:

0.643

Gnomad4 EAS

AF:

0.693

Gnomad4 SAS

AF:

0.776

Gnomad4 FIN

AF:

0.696

Gnomad4 NFE

AF:

0.729

Gnomad4 OTH

AF:

0.741

Alfa

AF:

0.734

Hom.:

31324

Bravo

AF:

0.757

Asia WGS

AF:

0.743

AC:

2585

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

1.5

DANN

Benign

0.79

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over