GeneBe

ENST00000565079.5:c.-26+12011A>G

Variant names:

Variant summary

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

The ENST00000565079.5(MEAK7):​c.-26+12011A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,188 control chromosomes in the GnomAD database, including 49,534 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 0.79 ( 49534 hom., cov: 33)

Consequence

MEAK7
ENST00000565079.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.79

Publications

1 publications found
Variant links:
Genes affected
MEAK7 (HGNC:29325): (MTOR associated protein, eak-7 homolog) Involved in several processes, including TOR signaling; positive regulation of protein localization to lysosome; and response to insulin. Located in cytosol; lysosomal membrane; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

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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=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MEAK7ENST00000565079.5 linkc.-26+12011A>G intron_variant Intron 1 of 3 4 ENSP00000457557.1

Frequencies

GnomAD3 genomes
AF:
0.787
AC:
119661
AN:
152070
Hom.:
49517
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.542
Gnomad AMI
AF:
0.888
Gnomad AMR
AF:
0.784
Gnomad ASJ
AF:
0.923
Gnomad EAS
AF:
0.490
Gnomad SAS
AF:
0.794
Gnomad FIN
AF:
0.926
Gnomad MID
AF:
0.845
Gnomad NFE
AF:
0.927
Gnomad OTH
AF:
0.800
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.787
AC:
119716
AN:
152188
Hom.:
49534
Cov.:
33
AF XY:
0.785
AC XY:
58384
AN XY:
74404
show subpopulations
African (AFR)
AF:
0.542
AC:
22472
AN:
41458
American (AMR)
AF:
0.784
AC:
11986
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.923
AC:
3205
AN:
3472
East Asian (EAS)
AF:
0.490
AC:
2538
AN:
5176
South Asian (SAS)
AF:
0.795
AC:
3831
AN:
4818
European-Finnish (FIN)
AF:
0.926
AC:
9835
AN:
10616
Middle Eastern (MID)
AF:
0.854
AC:
251
AN:
294
European-Non Finnish (NFE)
AF:
0.927
AC:
63102
AN:
68038
Other (OTH)
AF:
0.798
AC:
1686
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1079
2158
3236
4315
5394
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
852
1704
2556
3408
4260
<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:
0.883
Hom.:
16428
Bravo
AF:
0.760
Asia WGS
AF:
0.634
AC:
2207
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.11
DANN
Benign
0.60
PhyloP100
-1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs451480; hg19: chr16-84575541; API