rs755087452
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_080632.3(UPF3B):āc.883T>Cā(p.Leu295Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000744 in 1,209,458 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 29 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_080632.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UPF3B | NM_080632.3 | c.883T>C | p.Leu295Leu | synonymous_variant | 9/11 | ENST00000276201.7 | NP_542199.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UPF3B | ENST00000276201.7 | c.883T>C | p.Leu295Leu | synonymous_variant | 9/11 | 1 | NM_080632.3 | ENSP00000276201.3 | ||
UPF3B | ENST00000345865.6 | c.844T>C | p.Leu282Leu | synonymous_variant | 8/10 | 1 | ENSP00000245418.2 | |||
UPF3B | ENST00000478840.1 | n.523T>C | non_coding_transcript_exon_variant | 6/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000268 AC: 3AN: 112002Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34200
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 182865Hom.: 0 AF XY: 0.0000445 AC XY: 3AN XY: 67381
GnomAD4 exome AF: 0.0000793 AC: 87AN: 1097456Hom.: 0 Cov.: 31 AF XY: 0.0000772 AC XY: 28AN XY: 362880
GnomAD4 genome AF: 0.0000268 AC: 3AN: 112002Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34200
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 25, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 25, 2015 | - - |
Syndromic X-linked intellectual disability 14 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 12, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2018 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at