rs5918520
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001034853.2(RPGR):c.1507-101A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 158,578 control chromosomes in the GnomAD database, including 4,584 homozygotes. There are 11,532 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.29 ( 2915 hom., 7318 hem., cov: 19)
Exomes 𝑓: 0.26 ( 1669 hom. 4214 hem. )
Consequence
RPGR
NM_001034853.2 intron
NM_001034853.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.283
Genes affected
RPGR (HGNC:10295): (retinitis pigmentosa GTPase regulator) This gene encodes a protein with a series of six RCC1-like domains (RLDs), characteristic of the highly conserved guanine nucleotide exchange factors. The encoded protein is found in the Golgi body and interacts with RPGRIP1. This protein localizes to the outer segment of rod photoreceptors and is essential for their viability. Mutations in this gene have been associated with X-linked retinitis pigmentosa (XLRP). Multiple alternatively spliced transcript variants that encode different isoforms of this gene have been reported, but the full-length natures of only some have been determined. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
Variant X-38291125-T-A is Benign according to our data. Variant chrX-38291125-T-A is described in ClinVar as [Benign]. Clinvar id is 1286105.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPGR | NM_001034853.2 | c.1507-101A>T | intron_variant | ENST00000645032.1 | NP_001030025.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPGR | ENST00000645032.1 | c.1507-101A>T | intron_variant | NM_001034853.2 | ENSP00000495537 | A2 |
Frequencies
GnomAD3 genomes AF: 0.295 AC: 27591AN: 93675Hom.: 2913 Cov.: 19 AF XY: 0.283 AC XY: 7320AN XY: 25901
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GnomAD4 exome AF: 0.259 AC: 16812AN: 64923Hom.: 1669 AF XY: 0.281 AC XY: 4214AN XY: 14995
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GnomAD4 genome AF: 0.295 AC: 27591AN: 93655Hom.: 2915 Cov.: 19 AF XY: 0.283 AC XY: 7318AN XY: 25897
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at