rs9907196

chr17-12081022-C-T

Variant summary

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

The NM_003010.4(MAP2K4):c.219-334C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,204 control chromosomes in the GnomAD database, including 2,595 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 0.17 (2595 hom., cov: 32)
• Consequence: MAP2K4 NM_003010.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

MAP2K4 (HGNC:6844): (mitogen-activated protein kinase kinase 4) This gene encodes a member of the mitogen-activated protein kinase (MAPK) family. Members of this family 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. They form a three-tiered signaling module composed of MAPKKKs, MAPKKs, and MAPKs. This protein is phosphorylated at serine and threonine residues by MAPKKKs and subsequently phosphorylates downstream MAPK targets at threonine and tyrosine residues. A similar protein in mouse has been reported to play a role in liver organogenesis. A pseudogene of this gene is located on the long arm of chromosome X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP2K4	NM_003010.4	c.219-334C>T		intron_variant		ENST00000353533.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP2K4	ENST00000353533.10	c.219-334C>T		intron_variant		1	NM_003010.4	P2

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26066 AN: 152086 Hom.: 2592 Cov.: 32

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.171 AC: 26068 AN: 152204 Hom.: 2595 Cov.: 32 AF XY: 0.172 AC XY: 12768 AN XY: 74424

Gnomad4 AFR AF: 0.0751

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.197

Alfa AF: 0.199 Hom.: 815

Bravo AF: 0.166

Asia WGS AF: 0.220 AC: 763 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.52
Dann	Benign	0.16

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: rs9907196; hg19: chr17-11984339; COSMIC: COSV62255963; COSMIC: COSV62255963;