15-89209963-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000326.5(RLBP1):c.*322C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 392,554 control chromosomes in the GnomAD database, including 437 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.038 ( 372 hom., cov: 32)
Exomes 𝑓: 0.0058 ( 65 hom. )
Consequence
RLBP1
NM_000326.5 3_prime_UTR
NM_000326.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0720
Genes affected
RLBP1 (HGNC:10024): (retinaldehyde binding protein 1) The protein encoded by this gene is a 36-kD water-soluble protein which carries 11-cis-retinaldehyde or 11-cis-retinal as physiologic ligands. It may be a functional component of the visual cycle. Mutations of this gene have been associated with severe rod-cone dystrophy, Bothnia dystrophy (nonsyndromic autosomal recessive retinitis pigmentosa) and retinitis punctata albescens. [provided by RefSeq, Jul 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=-0.87).
BP6
Variant 15-89209963-G-A is Benign according to our data. Variant chr15-89209963-G-A is described in ClinVar as [Benign]. Clinvar id is 317227.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RLBP1 | NM_000326.5 | c.*322C>T | 3_prime_UTR_variant | 9/9 | ENST00000268125.10 | NP_000317.1 | ||
RLBP1 | XM_011521870.3 | c.*322C>T | 3_prime_UTR_variant | 9/9 | XP_011520172.1 | |||
RLBP1 | XM_047432927.1 | c.*322C>T | 3_prime_UTR_variant | 7/7 | XP_047288883.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RLBP1 | ENST00000268125 | c.*322C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_000326.5 | ENSP00000268125.5 | |||
RLBP1 | ENST00000563254.1 | c.*322C>T | downstream_gene_variant | 2 | ENSP00000454740.1 |
Frequencies
GnomAD3 genomes AF: 0.0378 AC: 5755AN: 152188Hom.: 372 Cov.: 32
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GnomAD4 exome AF: 0.00577 AC: 1386AN: 240248Hom.: 65 Cov.: 0 AF XY: 0.00513 AC XY: 651AN XY: 126854
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GnomAD4 genome AF: 0.0379 AC: 5769AN: 152306Hom.: 372 Cov.: 32 AF XY: 0.0364 AC XY: 2709AN XY: 74480
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Pigmentary retinal dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 13, 2018 | 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). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Newfoundland cone-rod dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 13, 2018 | 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). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Retinitis pigmentosa Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 13, 2018 | 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). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
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