21-46287125-TAAA-TAA

Variant summary

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

The ENST00000397701.9(YBEY):​c.210+3delA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,489,962 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000027 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0011 ( 0 hom. )

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+12delA 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+3delA splice_region_variant, intron_variant Intron 2 of 4 2 NM_001314025.2 ENSP00000380813.4 P58557-1

Frequencies

GnomAD3 genomes
AF:
0.0000268
AC:
4
AN:
149396
Hom.:
0
Cov.:
0
show subpopulations
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:
0.000421
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000297
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00112
AC:
1507
AN:
1340566
Hom.:
0
Cov.:
31
AF XY:
0.00119
AC XY:
791
AN XY:
664034
show subpopulations
Gnomad4 AFR exome
AF:
0.00243
Gnomad4 AMR exome
AF:
0.00375
Gnomad4 ASJ exome
AF:
0.00220
Gnomad4 EAS exome
AF:
0.00111
Gnomad4 SAS exome
AF:
0.00265
Gnomad4 FIN exome
AF:
0.00117
Gnomad4 NFE exome
AF:
0.000885
Gnomad4 OTH exome
AF:
0.00105
GnomAD4 genome
AF:
0.0000268
AC:
4
AN:
149396
Hom.:
0
Cov.:
0
AF XY:
0.0000413
AC XY:
3
AN XY:
72632
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000421
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000297
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs58271568; hg19: chr21-47707039; API