rs8069375
Positions:
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1
The NM_014336.5(AIPL1):c.341C>T(p.Thr114Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00306 in 1,613,962 control chromosomes in the GnomAD database, including 127 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.016 ( 76 hom., cov: 33)
Exomes 𝑓: 0.0017 ( 51 hom. )
Consequence
AIPL1
NM_014336.5 missense
NM_014336.5 missense
Scores
7
11
Clinical Significance
Conservation
PhyloP100: 4.83
Genes affected
AIPL1 (HGNC:359): (aryl hydrocarbon receptor interacting protein like 1) Leber congenital amaurosis (LCA) is the most severe inherited retinopathy with the earliest age of onset and accounts for at least 5% of all inherited retinal diseases. Affected individuals are diagnosed at birth or in the first few months of life with nystagmus, severely impaired vision or blindness and an abnormal or flat electroretinogram. The photoreceptor/pineal-expressed gene, AIPL1, encoding aryl-hydrocarbon interacting protein-like 1, is located within the LCA4 candidate region. The encoded protein contains three tetratricopeptide motifs, consistent with chaperone or nuclear transport activity. Mutations in this gene may cause approximately 20% of recessive LCA. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
PM1
?
In a domain PPIase FKBP-type (size 92) in uniprot entity AIPL1_HUMAN there are 24 pathogenic changes around while only 7 benign (77%) in NM_014336.5
BP4
?
Computational evidence support a benign effect (MetaRNN=0.005100429).
BP6
?
Variant 17-6428442-G-A is Benign according to our data. Variant chr17-6428442-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 99801.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-6428442-G-A is described in Lovd as [Likely_pathogenic]. Variant chr17-6428442-G-A is described in Lovd as [Likely_benign]. Variant chr17-6428442-G-A is described in Lovd as [Pathogenic].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0545 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIPL1 | NM_014336.5 | c.341C>T | p.Thr114Ile | missense_variant | 3/6 | ENST00000381129.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIPL1 | ENST00000381129.8 | c.341C>T | p.Thr114Ile | missense_variant | 3/6 | 1 | NM_014336.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0162 AC: 2466AN: 152236Hom.: 74 Cov.: 33
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GnomAD3 exomes AF: 0.00412 AC: 1034AN: 251086Hom.: 28 AF XY: 0.00289 AC XY: 393AN XY: 135756
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GnomAD4 exome AF: 0.00169 AC: 2466AN: 1461608Hom.: 51 Cov.: 31 AF XY: 0.00143 AC XY: 1038AN XY: 727120
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GnomAD4 genome ? AF: 0.0162 AC: 2475AN: 152354Hom.: 76 Cov.: 33 AF XY: 0.0159 AC XY: 1184AN XY: 74496
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:8Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 28, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 18, 2022 | - - |
Leber congenital amaurosis 4 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
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. - |
not provided Benign:1Other:1
not provided, no classification provided | literature only | Retina International | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 13, 2019 | This variant is associated with the following publications: (PMID: 10873396, 33067476, 27884173, 20981092) - |
Retinitis Pigmentosa, Recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Retinitis pigmentosa;C1858386:Leber congenital amaurosis 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 05, 2022 | - - |
Retinitis pigmentosa Benign: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). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.;.;.;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.;L;.;.;.
MutationTaster
Benign
D;D;D;D;D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;.;.;.;.;.;.;.
REVEL
Uncertain
Sift
Benign
T;.;.;.;.;.;.;.
Sift4G
Benign
T;T;T;T;T;T;T;.
Polyphen
P;.;P;.;.;P;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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