21-29111830-T-G

Variant summary

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

The NM_020152.4(MAP3K7CL):​c.370+19249T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,994 control chromosomes in the GnomAD database, including 18,829 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 0.50 ( 18829 hom., cov: 31)

Consequence

MAP3K7CL
NM_020152.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.230
Variant links:
Genes affected
MAP3K7CL (HGNC:16457): (MAP3K7 C-terminal like) Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAP3K7CLNM_001286634.2 linkc.370+19249T>G intron_variant Intron 5 of 7 NP_001273563.1 P57077-1B0EVZ6
MAP3K7CLNM_001371369.1 linkc.370+19249T>G intron_variant Intron 6 of 8 NP_001358298.1
MAP3K7CLNM_020152.4 linkc.370+19249T>G intron_variant Intron 7 of 9 NP_064537.1 P57077-1B0EVZ6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAP3K7CLENST00000341618.8 linkc.370+19249T>G intron_variant Intron 5 of 7 1 ENSP00000343212.4 P57077-1
MAP3K7CLENST00000399947.6 linkc.370+19249T>G intron_variant Intron 6 of 8 1 ENSP00000382828.2 P57077-1
MAP3K7CLENST00000339024.8 linkc.-169+2647T>G intron_variant Intron 2 of 6 2 ENSP00000345777.4 P57077-4

Frequencies

GnomAD3 genomes
AF:
0.496
AC:
75348
AN:
151876
Hom.:
18822
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.461
Gnomad AMI
AF:
0.364
Gnomad AMR
AF:
0.510
Gnomad ASJ
AF:
0.466
Gnomad EAS
AF:
0.636
Gnomad SAS
AF:
0.411
Gnomad FIN
AF:
0.482
Gnomad MID
AF:
0.576
Gnomad NFE
AF:
0.514
Gnomad OTH
AF:
0.521
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.496
AC:
75401
AN:
151994
Hom.:
18829
Cov.:
31
AF XY:
0.494
AC XY:
36690
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.461
Gnomad4 AMR
AF:
0.511
Gnomad4 ASJ
AF:
0.466
Gnomad4 EAS
AF:
0.637
Gnomad4 SAS
AF:
0.411
Gnomad4 FIN
AF:
0.482
Gnomad4 NFE
AF:
0.514
Gnomad4 OTH
AF:
0.518
Alfa
AF:
0.507
Hom.:
3140
Bravo
AF:
0.498
Asia WGS
AF:
0.517
AC:
1801
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.4
DANN
Benign
0.45

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: rs2832186; hg19: chr21-30484151; API