19-7910319-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_145185.4(MAP2K7):c.393C>T(p.Cys131=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00539 in 1,613,268 control chromosomes in the GnomAD database, including 368 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.028 ( 208 hom., cov: 33)
Exomes 𝑓: 0.0030 ( 160 hom. )
Consequence
MAP2K7
NM_145185.4 synonymous
NM_145185.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.97
Genes affected
MAP2K7 (HGNC:6847): (mitogen-activated protein kinase kinase 7) The protein encoded by this gene is a dual specificity protein kinase that belongs to the MAP kinase kinase family. This kinase specifically activates MAPK8/JNK1 and MAPK9/JNK2, and this kinase itself is phosphorylated and activated by MAP kinase kinase kinases including MAP3K1/MEKK1, MAP3K2/MEKK2,MAP3K3/MEKK5, and MAP4K2/GCK. This kinase is involved in the signal transduction mediating the cell responses to proinflammatory cytokines, and environmental stresses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
Variant 19-7910319-C-T is Benign according to our data. Variant chr19-7910319-C-T is described in ClinVar as [Benign]. Clinvar id is 777407.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.97 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0929 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP2K7 | NM_145185.4 | c.393C>T | p.Cys131= | synonymous_variant | 4/11 | ENST00000397979.4 | |
MAP2K7 | NM_001297555.2 | c.441C>T | p.Cys147= | synonymous_variant | 5/12 | ||
MAP2K7 | NM_001297556.2 | c.393C>T | p.Cys131= | synonymous_variant | 4/11 | ||
MAP2K7 | XM_006722800.3 | c.441C>T | p.Cys147= | synonymous_variant | 5/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2K7 | ENST00000397979.4 | c.393C>T | p.Cys131= | synonymous_variant | 4/11 | 1 | NM_145185.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0282 AC: 4287AN: 152198Hom.: 208 Cov.: 33
GnomAD3 genomes
AF:
AC:
4287
AN:
152198
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00749 AC: 1855AN: 247782Hom.: 90 AF XY: 0.00566 AC XY: 764AN XY: 135004
GnomAD3 exomes
AF:
AC:
1855
AN:
247782
Hom.:
AF XY:
AC XY:
764
AN XY:
135004
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00301 AC: 4402AN: 1460952Hom.: 160 Cov.: 34 AF XY: 0.00258 AC XY: 1876AN XY: 726776
GnomAD4 exome
AF:
AC:
4402
AN:
1460952
Hom.:
Cov.:
34
AF XY:
AC XY:
1876
AN XY:
726776
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0282 AC: 4293AN: 152316Hom.: 208 Cov.: 33 AF XY: 0.0275 AC XY: 2051AN XY: 74470
GnomAD4 genome
AF:
AC:
4293
AN:
152316
Hom.:
Cov.:
33
AF XY:
AC XY:
2051
AN XY:
74470
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
15
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at