rs143538947
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_080632.3(UPF3B):c.1121G>A(p.Arg374His) variant causes a missense change. The variant allele was found at a frequency of 0.000539 in 1,208,797 control chromosomes in the GnomAD database, including 2 homozygotes. There are 179 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R374C) has been classified as Likely benign.
Frequency
Consequence
NM_080632.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UPF3B | NM_080632.3 | c.1121G>A | p.Arg374His | missense_variant | 10/11 | ENST00000276201.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UPF3B | ENST00000276201.7 | c.1121G>A | p.Arg374His | missense_variant | 10/11 | 1 | NM_080632.3 | A1 | |
UPF3B | ENST00000345865.6 | c.1082G>A | p.Arg361His | missense_variant | 9/10 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00159 AC: 177AN: 111160Hom.: 1 Cov.: 22 AF XY: 0.00129 AC XY: 43AN XY: 33356
GnomAD3 exomes AF: 0.000521 AC: 95AN: 182342Hom.: 0 AF XY: 0.000418 AC XY: 28AN XY: 66934
GnomAD4 exome AF: 0.000433 AC: 475AN: 1097582Hom.: 1 Cov.: 31 AF XY: 0.000375 AC XY: 136AN XY: 363042
GnomAD4 genome AF: 0.00159 AC: 177AN: 111215Hom.: 1 Cov.: 22 AF XY: 0.00129 AC XY: 43AN XY: 33421
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 09, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 14, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 30, 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. - |
Syndromic X-linked intellectual disability 14 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 23, 2016 | This alteration is classified as 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