rs150125

Variant summary

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

The NM_145331.3(MAP3K7):​c.1357-5501G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 151,932 control chromosomes in the GnomAD database, including 38,332 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 0.71 ( 38332 hom., cov: 31)

Consequence

MAP3K7
NM_145331.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.395
Variant links:
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]

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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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAP3K7NM_145331.3 linkuse as main transcriptc.1357-5501G>A intron_variant ENST00000369329.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAP3K7ENST00000369329.8 linkuse as main transcriptc.1357-5501G>A intron_variant 1 NM_145331.3 P3O43318-1

Frequencies

GnomAD3 genomes
AF:
0.707
AC:
107351
AN:
151814
Hom.:
38305
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.767
Gnomad AMI
AF:
0.644
Gnomad AMR
AF:
0.644
Gnomad ASJ
AF:
0.811
Gnomad EAS
AF:
0.469
Gnomad SAS
AF:
0.694
Gnomad FIN
AF:
0.638
Gnomad MID
AF:
0.810
Gnomad NFE
AF:
0.708
Gnomad OTH
AF:
0.748
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.707
AC:
107432
AN:
151932
Hom.:
38332
Cov.:
31
AF XY:
0.701
AC XY:
52018
AN XY:
74232
show subpopulations
Gnomad4 AFR
AF:
0.767
Gnomad4 AMR
AF:
0.645
Gnomad4 ASJ
AF:
0.811
Gnomad4 EAS
AF:
0.470
Gnomad4 SAS
AF:
0.694
Gnomad4 FIN
AF:
0.638
Gnomad4 NFE
AF:
0.708
Gnomad4 OTH
AF:
0.751
Alfa
AF:
0.703
Hom.:
26657
Bravo
AF:
0.707
Asia WGS
AF:
0.639
AC:
2226
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.22
DANN
Benign
0.57

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: rs150125; hg19: chr6-91239003; API