rs2233072

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002749.4(MAPK7):​c.-121T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 1,094,862 control chromosomes in the GnomAD database, including 301,679 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 0.55 ( 28969 hom., cov: 32)
Exomes 𝑓: 0.75 ( 272710 hom. )

Consequence

MAPK7
NM_002749.4 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.202
Variant links:
Genes affected
MAPK7 (HGNC:6880): (mitogen-activated protein kinase 7) 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 specifically activated by mitogen-activated protein kinase kinase 5 (MAP2K5/MEK5). It is involved in the downstream signaling processes of various receptor molecules including receptor type kinases, and G protein-coupled receptors. In response to extracelluar signals, this kinase translocates to cell nucleus, where it regulates gene expression by phosphorylating, and activating different transcription factors. Four alternatively spliced transcript variants of this gene encoding two distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAPK7NM_002749.4 linkuse as main transcriptc.-121T>G 5_prime_UTR_variant 1/7 ENST00000395604.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAPK7ENST00000395604.8 linkuse as main transcriptc.-121T>G 5_prime_UTR_variant 1/71 NM_002749.4 P1Q13164-1

Frequencies

GnomAD3 genomes
AF:
0.546
AC:
82972
AN:
152038
Hom.:
28973
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.167
Gnomad AMI
AF:
0.934
Gnomad AMR
AF:
0.530
Gnomad ASJ
AF:
0.828
Gnomad EAS
AF:
0.00578
Gnomad SAS
AF:
0.338
Gnomad FIN
AF:
0.743
Gnomad MID
AF:
0.649
Gnomad NFE
AF:
0.783
Gnomad OTH
AF:
0.604
GnomAD4 exome
AF:
0.746
AC:
703580
AN:
942706
Hom.:
272710
Cov.:
44
AF XY:
0.743
AC XY:
329341
AN XY:
443502
show subpopulations
Gnomad4 AFR exome
AF:
0.120
Gnomad4 AMR exome
AF:
0.487
Gnomad4 ASJ exome
AF:
0.823
Gnomad4 EAS exome
AF:
0.00461
Gnomad4 SAS exome
AF:
0.381
Gnomad4 FIN exome
AF:
0.744
Gnomad4 NFE exome
AF:
0.787
Gnomad4 OTH exome
AF:
0.669
GnomAD4 genome
AF:
0.545
AC:
82962
AN:
152156
Hom.:
28969
Cov.:
32
AF XY:
0.534
AC XY:
39738
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.166
Gnomad4 AMR
AF:
0.529
Gnomad4 ASJ
AF:
0.828
Gnomad4 EAS
AF:
0.00599
Gnomad4 SAS
AF:
0.340
Gnomad4 FIN
AF:
0.743
Gnomad4 NFE
AF:
0.783
Gnomad4 OTH
AF:
0.596
Alfa
AF:
0.728
Hom.:
38289
Bravo
AF:
0.516
Asia WGS
AF:
0.166
AC:
580
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
8.3
DANN
Benign
0.60

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs2233072; hg19: chr17-19281828; API