21-46287125-TAAA-TAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000397701.9(YBEY):​c.210+2_210+3insAAAAAAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000092 in 1,359,226 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 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000092 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

YBEY
ENST00000397701.9 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.890
Variant links:
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 made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
YBEYNM_001314025.2 linkc.210+5_210+12dupAAAAAAAA intron_variant Intron 2 of 4 ENST00000397701.9 NP_001300954.1 P58557-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
YBEYENST00000397701.9 linkc.210+2_210+3insAAAAAAAA splice_region_variant, intron_variant Intron 2 of 4 2 NM_001314025.2 ENSP00000380813.4 P58557-1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
149398
Hom.:
0
Cov.:
0
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000920
AC:
125
AN:
1359226
Hom.:
0
Cov.:
31
AF XY:
0.0000905
AC XY:
61
AN XY:
673804
show subpopulations
Gnomad4 AFR exome
AF:
0.0000338
Gnomad4 AMR exome
AF:
0.000222
Gnomad4 ASJ exome
AF:
0.0000431
Gnomad4 EAS exome
AF:
0.0000824
Gnomad4 SAS exome
AF:
0.0000924
Gnomad4 FIN exome
AF:
0.000164
Gnomad4 NFE exome
AF:
0.0000931
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
149398
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
72636
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr21-47707039; API