rs55712755
Positions:
- chrX-119851748-CTTTTT-C
- chrX-119851748-CTTTTT-CT
- chrX-119851748-CTTTTT-CTT
- chrX-119851748-CTTTTT-CTTT
- chrX-119851748-CTTTTT-CTTTT
- chrX-119851748-CTTTTT-CTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-119851748-CTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1
The NM_080632.3(UPF3B):c.263+14_263+18del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000127 in 495,297 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., 0 hem., cov: 0)
Exomes 𝑓: 0.00013 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
UPF3B
NM_080632.3 intron
NM_080632.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.277
Genes affected
UPF3B (HGNC:20439): (UPF3B regulator of nonsense mediated mRNA decay) This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome X. Two splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.000127 (63/495297) while in subpopulation AMR AF= 0.000164 (2/12180). AF 95% confidence interval is 0.000117. There are 0 homozygotes in gnomad4_exome. There are 0 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UPF3B | NM_080632.3 | c.263+14_263+18del | intron_variant | ENST00000276201.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UPF3B | ENST00000276201.7 | c.263+14_263+18del | intron_variant | 1 | NM_080632.3 | A1 | |||
UPF3B | ENST00000345865.6 | c.263+14_263+18del | intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 64224Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 11402 FAILED QC
GnomAD3 genomes
?
AF:
AC:
0
AN:
64224
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
11402
FAILED QC
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:
GnomAD4 exome AF: 0.000127 AC: 63AN: 495297Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 145725
GnomAD4 exome
AF:
AC:
63
AN:
495297
Hom.:
AF XY:
AC XY:
0
AN XY:
145725
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 64224Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 11402
GnomAD4 genome
?
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
64224
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
11402
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at