10-48425832-T-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001323329.2(MAPK8):c.689-56T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,844 control chromosomes in the GnomAD database, including 19,835 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.50 (19835 hom., cov: 32)
  • Exomes 𝑓: 0.52 (113383 hom.)
  • Failed GnomAD Quality Control
• Consequence: MAPK8 NM_001323329.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.01

Genes affected

MAPK8 (HGNC:6881): (mitogen-activated protein kinase 8) 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 cell stimuli, and targets specific transcription factors, and thus mediates immediate-early gene expression in response to cell stimuli. The activation of this kinase by tumor-necrosis factor alpha (TNF-alpha) is found to be required for TNF-alpha induced apoptosis. This kinase is also involved in UV radiation induced apoptosis, which is thought to be related to cytochrom c-mediated cell death pathway. Studies of the mouse counterpart of this gene suggested that this kinase play a key role in T cell proliferation, apoptosis and differentiation. Several alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP6: Variant 10-48425832-T-A is Benign according to our data. Variant chr10-48425832-T-A is described in ClinVar as [Benign]. Clinvar id is 1241915.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAPK8	NM_001323329.2	c.689-56T>A		intron_variant		ENST00000374189.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPK8	ENST00000374189.6	c.689-56T>A		intron_variant		5	NM_001323329.2	A1

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76378 AN: 151726 Hom.: 19835 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.539

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.524 AC: 423260 AN: 807754 Hom.: 113383 Cov.: 10 AF XY: 0.522 AC XY: 213972 AN XY: 409660

Gnomad4 AFR exome AF: 0.343

Gnomad4 AMR exome AF: 0.488

Gnomad4 ASJ exome AF: 0.560

Gnomad4 EAS exome AF: 0.649

Gnomad4 SAS exome AF: 0.364

Gnomad4 FIN exome AF: 0.518

Gnomad4 NFE exome AF: 0.534

Gnomad4 OTH exome AF: 0.531

GnomAD4 genome AF: 0.503 AC: 76403 AN: 151844 Hom.: 19835 Cov.: 32 AF XY: 0.503 AC XY: 37294 AN XY: 74190

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.533

Alfa AF: 0.142 Hom.: 572

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 26, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	15
Dann	Benign	0.72

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: rs201968887; hg19: chr10-49633875;