rs884202

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_145160.3(MAP2K5):​c.1135-7552G>A variant causes a intron change. The variant allele was found at a frequency of 0.62 in 152,052 control chromosomes in the GnomAD database, including 29,979 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 0.62 ( 29979 hom., cov: 32)

Consequence

MAP2K5
NM_145160.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.74
Variant links:
Genes affected
MAP2K5 (HGNC:6845): (mitogen-activated protein kinase kinase 5) The protein encoded by this gene is a dual specificity protein kinase that belongs to the MAP kinase kinase family. This kinase specifically interacts with and activates MAPK7/ERK5. This kinase itself can be phosphorylated and activated by MAP3K3/MEKK3, as well as by atypical protein kinase C isoforms (aPKCs). The signal cascade mediated by this kinase is involved in growth factor stimulated cell proliferation and muscle cell differentiation. Three alternatively spliced transcript variants of this gene encoding distinct isoforms have been described. [provided by RefSeq, May 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAP2K5NM_145160.3 linkuse as main transcriptc.1135-7552G>A intron_variant ENST00000178640.10
MAP2K5NM_001206804.2 linkuse as main transcriptc.1027-7552G>A intron_variant
MAP2K5NM_002757.4 linkuse as main transcriptc.1105-7552G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAP2K5ENST00000178640.10 linkuse as main transcriptc.1135-7552G>A intron_variant 1 NM_145160.3 P1Q13163-1

Frequencies

GnomAD3 genomes
AF:
0.621
AC:
94296
AN:
151934
Hom.:
29965
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.598
Gnomad AMI
AF:
0.808
Gnomad AMR
AF:
0.468
Gnomad ASJ
AF:
0.546
Gnomad EAS
AF:
0.373
Gnomad SAS
AF:
0.552
Gnomad FIN
AF:
0.699
Gnomad MID
AF:
0.639
Gnomad NFE
AF:
0.682
Gnomad OTH
AF:
0.611
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.620
AC:
94339
AN:
152052
Hom.:
29979
Cov.:
32
AF XY:
0.616
AC XY:
45815
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.598
Gnomad4 AMR
AF:
0.467
Gnomad4 ASJ
AF:
0.546
Gnomad4 EAS
AF:
0.372
Gnomad4 SAS
AF:
0.551
Gnomad4 FIN
AF:
0.699
Gnomad4 NFE
AF:
0.682
Gnomad4 OTH
AF:
0.610
Alfa
AF:
0.657
Hom.:
55322
Bravo
AF:
0.598
Asia WGS
AF:
0.462
AC:
1607
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.29
CADD
Benign
18
DANN
Benign
0.76

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs884202; hg19: chr15-68054388; API