4-86046677-C-T

Variant names:

• chr4-86046677-C-T
• rs10028075
• NM_138982.4:c.1111-15246G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138982.4(MAPK10):​c.1111-15246G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,892 control chromosomes in the GnomAD database, including 15,623 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 0.45 (15623 hom., cov: 32)
• Consequence: MAPK10 NM_138982.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 5 publications found

Genes affected

MAPK10 (HGNC:6872): (mitogen-activated protein kinase 10) The protein encoded by this gene is a member of the MAP kinase family. MAP kinases act as integration points for multiple biochemical signals, and thus are involved in a wide variety of cellular processes, such as proliferation, differentiation, transcription regulation and development. This kinase is specifically expressed in a subset of neurons in the nervous system, and is activated by threonine and tyrosine phosphorylation. Targeted deletion of this gene in mice suggests that it may have a role in stress-induced neuronal apoptosis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. A recent study provided evidence for translational readthrough in this gene, and expression of an additional C-terminally extended isoform via the use of an alternative in-frame translation termination codon. [provided by RefSeq, Dec 2017]

MAPK10 Gene-Disease associations (from GenCC):

• Lennox-Gastaut syndrome

  Inheritance: AD Classification: LIMITED Submitted by: G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138982.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPK10	NM_138982.4	MANE Select	c.1111-15246G>A		intron	N/A	NP_620448.1
	MAPK10	NM_001318069.2		c.1111-15246G>A		intron	N/A	NP_001304998.1
	MAPK10	NM_001318067.1		c.1111-15246G>A		intron	N/A	NP_001304996.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPK10	ENST00000641462.2	MANE Select	c.1111-15246G>A		intron	N/A	ENSP00000493435.1
	MAPK10	ENST00000638225.1	TSL:1	c.997-15246G>A		intron	N/A	ENSP00000491866.1
	MAPK10	ENST00000395160.9	TSL:1	c.1111-15246G>A		intron	N/A	ENSP00000378589.5

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67539 AN: 151774 Hom.: 15614 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.401

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.445 AC: 67595 AN: 151892 Hom.: 15623 Cov.: 32 AF XY: 0.437 AC XY: 32423 AN XY: 74238

African (AFR) AF: 0.564 AC: 23336 AN: 41410

American (AMR) AF: 0.340 AC: 5179 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1271 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1829 AN: 5164

South Asian (SAS) AF: 0.327 AC: 1578 AN: 4824

European-Finnish (FIN) AF: 0.326 AC: 3434 AN: 10534

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29626 AN: 67932

Other (OTH) AF: 0.404 AC: 854 AN: 2114

Alfa AF: 0.432 Hom.: 7659

Bravo AF: 0.449

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.92
DANN	Benign	0.55
PhyloP100		-0.37
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10028075; hg19: chr4-86967830;