6-90550397-T-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145331.3(MAP3K7):c.949+71A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MAP3K7
NM_145331.3 intron
NM_145331.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.575
Publications
5 publications found
Genes affected
MAP3K7 (HGNC:6859): (mitogen-activated protein kinase kinase kinase 7) The protein encoded by this gene is a member of the serine/threonine protein kinase family. This kinase mediates the signaling transduction induced by TGF beta and morphogenetic protein (BMP), and controls a variety of cell functions including transcription regulation and apoptosis. In response to IL-1, this protein forms a kinase complex including TRAF6, MAP3K7P1/TAB1 and MAP3K7P2/TAB2; this complex is required for the activation of nuclear factor kappa B. This kinase can also activate MAPK8/JNK, MAP2K4/MKK4, and thus plays a role in the cell response to environmental stresses. Four alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
MAP3K7 Gene-Disease associations (from GenCC):
- cardiospondylocarpofacial syndromeInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)
- frontometaphyseal dysplasiaInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Illumina
- frontometaphyseal dysplasia 2Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 846454Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 439746
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
846454
Hom.:
AF XY:
AC XY:
0
AN XY:
439746
African (AFR)
AF:
AC:
0
AN:
20206
American (AMR)
AF:
AC:
0
AN:
28206
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
18976
East Asian (EAS)
AF:
AC:
0
AN:
35638
South Asian (SAS)
AF:
AC:
0
AN:
62132
European-Finnish (FIN)
AF:
AC:
0
AN:
47334
Middle Eastern (MID)
AF:
AC:
0
AN:
4346
European-Non Finnish (NFE)
AF:
AC:
0
AN:
590876
Other (OTH)
AF:
AC:
0
AN:
38740
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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