chrX-119851748-C-CTTTTT
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_080632.3(UPF3B):c.263+18_263+19insAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 52 hom., 176 hem., cov: 0)
Exomes 𝑓: 0.0016 ( 9 hom. 23 hem. )
Failed GnomAD Quality Control
Consequence
UPF3B
NM_080632.3 intron
NM_080632.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0650
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
Variant X-119851748-C-CTTTTT is Benign according to our data. Variant chrX-119851748-C-CTTTTT is described in ClinVar as [Benign]. Clinvar id is 2039555.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UPF3B | NM_080632.3 | c.263+18_263+19insAAAAA | intron_variant | ENST00000276201.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UPF3B | ENST00000276201.7 | c.263+18_263+19insAAAAA | intron_variant | 1 | NM_080632.3 | A1 | |||
UPF3B | ENST00000345865.6 | c.263+18_263+19insAAAAA | intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0127 AC: 813AN: 64215Hom.: 52 Cov.: 0 AF XY: 0.0153 AC XY: 174AN XY: 11403
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00157 AC: 777AN: 493981Hom.: 9 Cov.: 0 AF XY: 0.000159 AC XY: 23AN XY: 144775
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0127 AC: 814AN: 64207Hom.: 52 Cov.: 0 AF XY: 0.0154 AC XY: 176AN XY: 11401
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Syndromic X-linked intellectual disability 14 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at