GeneBe

chr21-29157697-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001286620.2(MAP3K7CL):​c.133-2244A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.032 in 152,294 control chromosomes in the GnomAD database, including 279 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 0.032 ( 279 hom., cov: 32)

Consequence

MAP3K7CL
NM_001286620.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.298

Publications

1 publications found
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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAP3K7CLNM_001286620.2 linkc.133-2244A>G intron_variant Intron 3 of 4 ENST00000399928.6 NP_001273549.1 P57077-4B0EVZ8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAP3K7CLENST00000399928.6 linkc.133-2244A>G intron_variant Intron 3 of 4 1 NM_001286620.2 ENSP00000382812.1 P57077-4

Frequencies

GnomAD3 genomes
AF:
0.0319
AC:
4862
AN:
152176
Hom.:
278
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.111
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0116
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.000426
Gnomad OTH
AF:
0.0249
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0320
AC:
4881
AN:
152294
Hom.:
279
Cov.:
32
AF XY:
0.0310
AC XY:
2312
AN XY:
74480
show subpopulations
African (AFR)
AF:
0.111
AC:
4615
AN:
41548
American (AMR)
AF:
0.0116
AC:
177
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3468
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5190
South Asian (SAS)
AF:
0.000415
AC:
2
AN:
4822
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10628
Middle Eastern (MID)
AF:
0.0204
AC:
6
AN:
294
European-Non Finnish (NFE)
AF:
0.000426
AC:
29
AN:
68018
Other (OTH)
AF:
0.0246
AC:
52
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
214
428
641
855
1069
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
52
104
156
208
260
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0306
Hom.:
23
Bravo
AF:
0.0370
Asia WGS
AF:
0.00664
AC:
23
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.7
DANN
Benign
0.58
PhyloP100
0.30
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs7283791; hg19: chr21-30530018; API