rs10807156

Positions:

• chr6-36037082-T-A
• chr6-36037082-T-C
• chr6-36037082-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139012.3(MAPK14):​c.116+8809T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,962 control chromosomes in the GnomAD database, including 3,915 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 0.20 (3915 hom., cov: 31)
• Consequence: MAPK14 NM_139012.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

MAPK14 (HGNC:6876): (mitogen-activated protein kinase 14) The protein encoded by this gene is a member of the MAP kinase family. MAP kinases act as an integration point for multiple biochemical signals, and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development. This kinase is activated by various environmental stresses and proinflammatory cytokines. The activation requires its phosphorylation by MAP kinase kinases (MKKs), or its autophosphorylation triggered by the interaction of MAP3K7IP1/TAB1 protein with this kinase. The substrates of this kinase include transcription regulator ATF2, MEF2C, and MAX, cell cycle regulator CDC25B, and tumor suppressor p53, which suggest the roles of this kinase in stress related transcription and cell cycle regulation, as well as in genotoxic stress response. Four alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAPK14	NM_139012.3	c.116+8809T>A		intron_variant		ENST00000229794.9	NP_620581.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAPK14	ENST00000229794.9	c.116+8809T>A		intron_variant		1	NM_139012.3	ENSP00000229794	P3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29976 AN: 151844 Hom.: 3909 Cov.: 31

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.197 AC: 29995 AN: 151962 Hom.: 3915 Cov.: 31 AF XY: 0.204 AC XY: 15149 AN XY: 74244

Gnomad4 AFR AF: 0.0669

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.213

Alfa AF: 0.202 Hom.: 460

Bravo AF: 0.201

Asia WGS AF: 0.340 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.052

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

Other links and lift over

dbSNP: rs10807156; hg19: chr6-36004859;