chrX-38286440-TTCCTCCTCTTCCCCCTCCCCTTCC-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBS1BS2
The NM_001034853.2(RPGR):βc.2535_2558delβ(p.Glu846_Glu853del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000289 in 689,456 control chromosomes in the GnomAD database, including 4 homozygotes. There are 52 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (β β ).
Frequency
Genomes: π 0.0011 ( 0 hom., 0 hem., cov: 3)
Exomes π: 0.00027 ( 4 hom. 52 hem. )
Consequence
RPGR
NM_001034853.2 inframe_deletion
NM_001034853.2 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.385
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 -14 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_001034853.2.
BP6
Variant X-38286440-TTCCTCCTCTTCCCCCTCCCCTTCC-T is Benign according to our data. Variant chrX-38286440-TTCCTCCTCTTCCCCCTCCCCTTCC-T is described in ClinVar as [Likely_benign]. Clinvar id is 445999.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00107 (15/14044) while in subpopulation AFR AF= 0.00548 (14/2554). AF 95% confidence interval is 0.00331. There are 0 homozygotes in gnomad4. There are 0 alleles in male gnomad4 subpopulation. Median coverage is 3. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 4 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPGR | NM_001034853.2 | c.2535_2558del | p.Glu846_Glu853del | inframe_deletion | 15/15 | ENST00000645032.1 | NP_001030025.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPGR | ENST00000645032.1 | c.2535_2558del | p.Glu846_Glu853del | inframe_deletion | 15/15 | NM_001034853.2 | ENSP00000495537 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00107 AC: 15AN: 14027Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0AN XY: 843
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GnomAD3 exomes AF: 0.000645 AC: 33AN: 51199Hom.: 3 AF XY: 0.000111 AC XY: 1AN XY: 9013
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GnomAD4 exome AF: 0.000272 AC: 184AN: 675412Hom.: 4 AF XY: 0.000279 AC XY: 52AN XY: 186466
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GnomAD4 genome AF: 0.00107 AC: 15AN: 14044Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0AN XY: 846
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 28, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 03, 2017 | - - |
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 26, 2024 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at