3-184711345-ATCCTCCTCC-A
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP3
The NM_022149.5(MAGEF1):c.468_476delGGAGGAGGA(p.Glu156_Glu158del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000255 in 1,567,478 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
MAGEF1
NM_022149.5 disruptive_inframe_deletion
NM_022149.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.29
Publications
12 publications found
Genes affected
MAGEF1 (HGNC:29639): (MAGE family member F1) This intronless gene encodes a member of the MAGE superfamily. It is ubiquitously expressed in normal tissues and in tumor cells. This gene includes a microsatellite repeat in the coding region. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_022149.5
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MAGEF1 | NM_022149.5 | c.468_476delGGAGGAGGA | p.Glu156_Glu158del | disruptive_inframe_deletion | Exon 1 of 1 | ENST00000317897.5 | NP_071432.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MAGEF1 | ENST00000317897.5 | c.468_476delGGAGGAGGA | p.Glu156_Glu158del | disruptive_inframe_deletion | Exon 1 of 1 | 6 | NM_022149.5 | ENSP00000315064.3 |
Frequencies
GnomAD3 genomes 0.00000665 AC: 1AN: 150448Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
150448
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00000825 AC: 2AN: 242436 AF XY: 0.00000761 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
242436
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000212 AC: 3AN: 1417030Hom.: 0 AF XY: 0.00000283 AC XY: 2AN XY: 705690 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1417030
Hom.:
AF XY:
AC XY:
2
AN XY:
705690
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33008
American (AMR)
AF:
AC:
1
AN:
44324
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25602
East Asian (EAS)
AF:
AC:
0
AN:
39552
South Asian (SAS)
AF:
AC:
0
AN:
84684
European-Finnish (FIN)
AF:
AC:
0
AN:
50978
Middle Eastern (MID)
AF:
AC:
0
AN:
5684
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1074246
Other (OTH)
AF:
AC:
1
AN:
58952
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
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75-80
>80
Age
GnomAD4 genome 0.00000665 AC: 1AN: 150448Hom.: 0 Cov.: 0 AF XY: 0.0000136 AC XY: 1AN XY: 73408 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
150448
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
73408
show subpopulations
African (AFR)
AF:
AC:
1
AN:
40870
American (AMR)
AF:
AC:
0
AN:
15146
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3454
East Asian (EAS)
AF:
AC:
0
AN:
5108
South Asian (SAS)
AF:
AC:
0
AN:
4744
European-Finnish (FIN)
AF:
AC:
0
AN:
10348
Middle Eastern (MID)
AF:
AC:
0
AN:
308
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67488
Other (OTH)
AF:
AC:
0
AN:
2076
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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