21-46302071-ATGGTGGTGGTGG-ATGGTGGTGGTGGTGGTGGTGG
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP3
The NM_058180.5(C21orf58):c.888_896dupCCACCACCA(p.His297_His299dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000312 in 1,506,750 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 0.000013 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000033 ( 0 hom. )
Consequence
C21orf58
NM_058180.5 disruptive_inframe_insertion
NM_058180.5 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.565
Publications
12 publications found
Genes affected
C21orf58 (HGNC:1300): (chromosome 21 open reading frame 58)
YBEY (HGNC:1299): (ybeY metalloendoribonuclease) This gene encodes a highly conserved metalloprotein. A similar protein in bacteria acts as an endoribonuclease, and is thought to function in ribosomal RNA maturation and ribosome assembly. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
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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_058180.5
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.0000132 AC: 2AN: 151408Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
151408
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: 0.0000179 AC: 2AN: 111606 AF XY: 0.0000165 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
111606
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000332 AC: 45AN: 1355342Hom.: 0 Cov.: 34 AF XY: 0.0000315 AC XY: 21AN XY: 667432 show subpopulations
GnomAD4 exome
AF:
AC:
45
AN:
1355342
Hom.:
Cov.:
34
AF XY:
AC XY:
21
AN XY:
667432
show subpopulations
African (AFR)
AF:
AC:
0
AN:
30746
American (AMR)
AF:
AC:
0
AN:
32382
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24368
East Asian (EAS)
AF:
AC:
5
AN:
34164
South Asian (SAS)
AF:
AC:
0
AN:
75966
European-Finnish (FIN)
AF:
AC:
0
AN:
42170
Middle Eastern (MID)
AF:
AC:
0
AN:
5500
European-Non Finnish (NFE)
AF:
AC:
37
AN:
1053756
Other (OTH)
AF:
AC:
3
AN:
56290
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.422
Heterozygous variant carriers
0
3
6
8
11
14
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000132 AC: 2AN: 151408Hom.: 0 Cov.: 0 AF XY: 0.0000135 AC XY: 1AN XY: 73878 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
151408
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
73878
show subpopulations
African (AFR)
AF:
AC:
2
AN:
41270
American (AMR)
AF:
AC:
0
AN:
15204
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3464
East Asian (EAS)
AF:
AC:
0
AN:
5116
South Asian (SAS)
AF:
AC:
0
AN:
4794
European-Finnish (FIN)
AF:
AC:
0
AN:
10506
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67760
Other (OTH)
AF:
AC:
0
AN:
2072
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
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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