rs41312110
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000339363.7(RPGR):c.2764+46C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0486 in 963,272 control chromosomes in the GnomAD database, including 1,001 homozygotes. There are 12,345 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.036 ( 87 hom., 1032 hem., cov: 22)
Exomes 𝑓: 0.050 ( 914 hom. 11313 hem. )
Consequence
RPGR
ENST00000339363.7 intron
ENST00000339363.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.39
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-38275043-G-A is Benign according to our data. Variant chrX-38275043-G-A is described in ClinVar as [Benign]. Clinvar id is 255834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-38275043-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.057 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPGR | NM_000328.3 | c.2149+46C>T | intron_variant | ||||
RPGR | NM_001367245.1 | c.2146+46C>T | intron_variant | ||||
RPGR | NM_001367246.1 | c.1963+46C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPGR | ENST00000339363.7 | c.2764+46C>T | intron_variant | 5 | P4 | ||||
RPGR | ENST00000494707.6 | c.1197+46C>T | intron_variant | 5 | |||||
RPGR | ENST00000642395.2 | c.2149+46C>T | intron_variant | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0362 AC: 4014AN: 110956Hom.: 87 Cov.: 22 AF XY: 0.0310 AC XY: 1031AN XY: 33222
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GnomAD3 exomes AF: 0.0372 AC: 6371AN: 171074Hom.: 106 AF XY: 0.0356 AC XY: 2065AN XY: 58036
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GnomAD4 exome AF: 0.0502 AC: 42765AN: 852268Hom.: 914 Cov.: 14 AF XY: 0.0474 AC XY: 11313AN XY: 238542
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GnomAD4 genome ? AF: 0.0362 AC: 4016AN: 111004Hom.: 87 Cov.: 22 AF XY: 0.0310 AC XY: 1032AN XY: 33280
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Retinitis pigmentosa 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Macular degeneration, X-linked atrophic Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 06, 2018 | - - |
X-linked cone-rod dystrophy 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at