rs73201156
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000382483.4(RP1L1):c.3955G>A(p.Ala1319Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0057 in 817,348 control chromosomes in the GnomAD database, including 112 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1319G) has been classified as Benign.
Frequency
Consequence
ENST00000382483.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RP1L1 | NM_178857.6 | c.3955G>A | p.Ala1319Thr | missense_variant | 4/4 | ENST00000382483.4 | NP_849188.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RP1L1 | ENST00000382483.4 | c.3955G>A | p.Ala1319Thr | missense_variant | 4/4 | 1 | NM_178857.6 | ENSP00000371923 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00519 AC: 390AN: 75110Hom.: 5 Cov.: 20
GnomAD3 exomes AF: 0.0150 AC: 1966AN: 131088Hom.: 67 AF XY: 0.0159 AC XY: 1113AN XY: 69934
GnomAD4 exome AF: 0.00576 AC: 4274AN: 742138Hom.: 107 Cov.: 90 AF XY: 0.00584 AC XY: 2202AN XY: 377036
GnomAD4 genome AF: 0.00516 AC: 388AN: 75210Hom.: 5 Cov.: 20 AF XY: 0.00565 AC XY: 215AN XY: 38086
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 10, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency (fails quality filter) - |
Occult macular dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Occult macular dystrophy;C5394208:Retinitis pigmentosa 88 Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 04, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at