15-89209963-G-A
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
Consequence
NM_000326.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RLBP1 | NM_000326.5 | c.*322C>T | 3_prime_UTR_variant | Exon 9 of 9 | ENST00000268125.10 | NP_000317.1 | ||
RLBP1 | XM_011521870.3 | c.*322C>T | 3_prime_UTR_variant | Exon 9 of 9 | XP_011520172.1 | |||
RLBP1 | XM_047432927.1 | c.*322C>T | 3_prime_UTR_variant | Exon 7 of 7 | XP_047288883.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0378 AC: 5755AN: 152188Hom.: 372 Cov.: 32
GnomAD4 exome AF: 0.00577 AC: 1386AN: 240248Hom.: 65 Cov.: 0 AF XY: 0.00513 AC XY: 651AN XY: 126854
GnomAD4 genome AF: 0.0379 AC: 5769AN: 152306Hom.: 372 Cov.: 32 AF XY: 0.0364 AC XY: 2709AN XY: 74480
ClinVar
Submissions by phenotype
Pigmentary retinal dystrophy Benign:1
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
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
- -
Retinitis pigmentosa Benign:1
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at