NM_001314025.2:c.210+11_210+12dupAA
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2
The NM_001314025.2(YBEY):c.210+11_210+12dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000511 in 1,506,712 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00057 ( 3 hom. )
Consequence
YBEY
NM_001314025.2 intron
NM_001314025.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.890
Publications
1 publications found
Genes affected
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: Likely_benign. The variant received -4 ACMG points.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001314025.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| YBEY | NM_001314025.2 | MANE Select | c.210+11_210+12dupAA | intron | N/A | NP_001300954.1 | P58557-1 | ||
| YBEY | NM_058181.3 | c.210+11_210+12dupAA | intron | N/A | NP_478061.1 | P58557-1 | |||
| YBEY | NM_001314022.2 | c.210+11_210+12dupAA | intron | N/A | NP_001300951.1 | P58557-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| YBEY | ENST00000397701.9 | TSL:2 MANE Select | c.210+2_210+3insAA | splice_region intron | N/A | ENSP00000380813.4 | P58557-1 | ||
| YBEY | ENST00000329319.7 | TSL:1 | c.210+2_210+3insAA | splice_region intron | N/A | ENSP00000329614.3 | P58557-1 | ||
| YBEY | ENST00000339195.10 | TSL:1 | c.210+2_210+3insAA | splice_region intron | N/A | ENSP00000340675.6 | P58557-2 |
Frequencies
GnomAD3 genomes 0.00000669 AC: 1AN: 149394Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
149394
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: 0.00298 AC: 406AN: 136068 AF XY: 0.00325 show subpopulations
GnomAD2 exomes
AF:
AC:
406
AN:
136068
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: 0.000567 AC: 769AN: 1357318Hom.: 3 Cov.: 31 AF XY: 0.000609 AC XY: 410AN XY: 672834 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
769
AN:
1357318
Hom.:
Cov.:
31
AF XY:
AC XY:
410
AN XY:
672834
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
10
AN:
29600
American (AMR)
AF:
AC:
50
AN:
31526
Ashkenazi Jewish (ASJ)
AF:
AC:
32
AN:
23144
East Asian (EAS)
AF:
AC:
7
AN:
36380
South Asian (SAS)
AF:
AC:
56
AN:
75680
European-Finnish (FIN)
AF:
AC:
38
AN:
48690
Middle Eastern (MID)
AF:
AC:
2
AN:
5042
European-Non Finnish (NFE)
AF:
AC:
550
AN:
1051290
Other (OTH)
AF:
AC:
24
AN:
55966
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.279
Heterozygous variant carriers
0
73
146
220
293
366
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
22
44
66
88
110
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00000669 AC: 1AN: 149394Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 72630 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
149394
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
72630
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
40688
American (AMR)
AF:
AC:
0
AN:
14992
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
3446
East Asian (EAS)
AF:
AC:
0
AN:
5126
South Asian (SAS)
AF:
AC:
0
AN:
4750
European-Finnish (FIN)
AF:
AC:
0
AN:
9728
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67392
Other (OTH)
AF:
AC:
0
AN:
2052
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
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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