rs28718831
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001034853.2(RPGR):c.1296A>T(p.Glu432Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,206,029 control chromosomes in the GnomAD database, including 13 homozygotes. There are 385 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001034853.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPGR | NM_001034853.2 | c.1296A>T | p.Glu432Asp | missense_variant | 11/15 | ENST00000645032.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPGR | ENST00000645032.1 | c.1296A>T | p.Glu432Asp | missense_variant | 11/15 | NM_001034853.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00659 AC: 725AN: 109961Hom.: 5 Cov.: 21 AF XY: 0.00574 AC XY: 185AN XY: 32217
GnomAD3 exomes AF: 0.00195 AC: 357AN: 183212Hom.: 4 AF XY: 0.00105 AC XY: 71AN XY: 67708
GnomAD4 exome AF: 0.000724 AC: 793AN: 1096016Hom.: 8 Cov.: 29 AF XY: 0.000551 AC XY: 199AN XY: 361442
GnomAD4 genome ? AF: 0.00661 AC: 727AN: 110013Hom.: 5 Cov.: 21 AF XY: 0.00576 AC XY: 186AN XY: 32279
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2015 | 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. - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 06, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 22, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at