rs17103671
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1
The NM_020366.4(RPGRIP1):āc.3341A>Gā(p.Asp1114Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00646 in 1,611,002 control chromosomes in the GnomAD database, including 265 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_020366.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPGRIP1 | NM_020366.4 | c.3341A>G | p.Asp1114Gly | missense_variant, splice_region_variant | 22/25 | ENST00000400017.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPGRIP1 | ENST00000400017.7 | c.3341A>G | p.Asp1114Gly | missense_variant, splice_region_variant | 22/25 | 1 | NM_020366.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0247 AC: 3763AN: 152178Hom.: 124 Cov.: 31
GnomAD3 exomes AF: 0.00836 AC: 2070AN: 247588Hom.: 54 AF XY: 0.00709 AC XY: 952AN XY: 134324
GnomAD4 exome AF: 0.00455 AC: 6640AN: 1458706Hom.: 141 Cov.: 29 AF XY: 0.00424 AC XY: 3075AN XY: 725684
GnomAD4 genome ? AF: 0.0248 AC: 3774AN: 152296Hom.: 124 Cov.: 31 AF XY: 0.0240 AC XY: 1790AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:5
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 19, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 10, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Leber congenital amaurosis 6 Pathogenic:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | May 15, 2005 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 27, 2021 | This variant is associated with the following publications: (PMID: 20981092, 27884173, 15800011, 11528500, 16272259, 29343940) - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
Leber congenital amaurosis 6;C2750720:Cone-rod dystrophy 13 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at