chrX-119851513-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_080632.3(UPF3B):c.352G>A(p.Val118Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000216 in 1,202,408 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_080632.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UPF3B | NM_080632.3 | c.352G>A | p.Val118Ile | missense_variant | 3/11 | ENST00000276201.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UPF3B | ENST00000276201.7 | c.352G>A | p.Val118Ile | missense_variant | 3/11 | 1 | NM_080632.3 | A1 | |
UPF3B | ENST00000345865.6 | c.352G>A | p.Val118Ile | missense_variant | 3/10 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000447 AC: 5AN: 111749Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33927
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183186Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67678
GnomAD4 exome AF: 0.0000202 AC: 22AN: 1090607Hom.: 0 Cov.: 28 AF XY: 0.0000168 AC XY: 6AN XY: 356715
GnomAD4 genome AF: 0.0000358 AC: 4AN: 111801Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1AN XY: 33989
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 03, 2017 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 27, 2018 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at