1-206717104-T-C

Variant names:

• chr1-206717104-T-C
• rs4256810
• NM_032960.4:c.280-11606T>C

Variant summary

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

The NM_032960.4(MAPKAPK2):​c.280-11606T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,116 control chromosomes in the GnomAD database, including 6,532 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 0.28 (6532 hom., cov: 32)
• Consequence: MAPKAPK2 NM_032960.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 16 publications found

Genes affected

MAPKAPK2 (HGNC:6887): (MAPK activated protein kinase 2) This gene encodes a member of the Ser/Thr protein kinase family. This kinase is regulated through direct phosphorylation by p38 MAP kinase. In conjunction with p38 MAP kinase, this kinase is known to be involved in many cellular processes including stress and inflammatory responses, nuclear export, gene expression regulation and cell proliferation. Heat shock protein HSP27 was shown to be one of the substrates of this kinase in vivo. Two transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAPKAPK2	NM_032960.4	c.280-11606T>C		intron_variant	Intron 1 of 9	ENST00000367103.4	NP_116584.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAPKAPK2	ENST00000367103.4	c.280-11606T>C		intron_variant	Intron 1 of 9	1	NM_032960.4	ENSP00000356070.4
MAPKAPK2	ENST00000294981.8	c.280-11606T>C		intron_variant	Intron 1 of 9	1		ENSP00000294981.4

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42786 AN: 151998 Hom.: 6534 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.281 AC: 42782 AN: 152116 Hom.: 6532 Cov.: 32 AF XY: 0.282 AC XY: 20966 AN XY: 74370

African (AFR) AF: 0.168 AC: 6987 AN: 41500

American (AMR) AF: 0.313 AC: 4791 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3470

East Asian (EAS) AF: 0.541 AC: 2799 AN: 5172

South Asian (SAS) AF: 0.242 AC: 1171 AN: 4830

European-Finnish (FIN) AF: 0.325 AC: 3436 AN: 10578

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21589 AN: 67966

Other (OTH) AF: 0.279 AC: 588 AN: 2110

Alfa AF: 0.312 Hom.: 30376

Bravo AF: 0.282

Asia WGS AF: 0.327 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.63
DANN	Benign	0.31
PhyloP100		0.079
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: rs4256810; hg19: chr1-206890449;