rs147649203
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000339363.7(RPGR):āc.2938A>Gā(p.Ile980Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000205 in 1,207,803 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 65 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I980T) has been classified as Likely benign.
Frequency
Consequence
ENST00000339363.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPGR | NM_000328.3 | c.2323A>G | p.Ile775Val | missense_variant | 19/19 | ||
RPGR | NM_001367245.1 | c.2320A>G | p.Ile774Val | missense_variant | 19/19 | ||
RPGR | NM_001367246.1 | c.2137A>G | p.Ile713Val | missense_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPGR | ENST00000339363.7 | c.2938A>G | p.Ile980Val | missense_variant | 18/18 | 5 | P4 | ||
RPGR | ENST00000642395.2 | c.2323A>G | p.Ile775Val | missense_variant | 19/19 | A2 | |||
RPGR | ENST00000644337.1 | c.2137A>G | p.Ile713Val | missense_variant | 18/18 |
Frequencies
GnomAD3 genomes AF: 0.000286 AC: 32AN: 111944Hom.: 0 Cov.: 23 AF XY: 0.000235 AC XY: 8AN XY: 34084
GnomAD3 exomes AF: 0.000191 AC: 35AN: 183156Hom.: 0 AF XY: 0.000177 AC XY: 12AN XY: 67686
GnomAD4 exome AF: 0.000197 AC: 216AN: 1095805Hom.: 0 Cov.: 29 AF XY: 0.000158 AC XY: 57AN XY: 361287
GnomAD4 genome AF: 0.000286 AC: 32AN: 111998Hom.: 0 Cov.: 23 AF XY: 0.000234 AC XY: 8AN XY: 34148
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 06, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 17, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at