rs2070139
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_005148.4(UNC119):c.*1C>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.156 in 1,613,854 control chromosomes in the GnomAD database, including 22,085 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.13 ( 1652 hom., cov: 32)
Exomes 𝑓: 0.16 ( 20433 hom. )
Consequence
UNC119
NM_005148.4 3_prime_UTR
NM_005148.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.17
Genes affected
UNC119 (HGNC:12565): (unc-119 lipid binding chaperone) This gene is specifically expressed in the photoreceptors in the retina. The encoded product shares strong homology with the C. elegans unc119 protein and it can functionally complement the C. elegans unc119 mutation. It has been localized to the photoreceptor synapses in the outer plexiform layer of the retina, and suggested to play a role in the mechanism of photoreceptor neurotransmitter release through the synaptic vesicle cycle. Two transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BP6
?
Variant 17-28547296-G-A is Benign according to our data. Variant chr17-28547296-G-A is described in ClinVar as [Benign]. Clinvar id is 259652.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC119 | NM_005148.4 | c.*1C>T | 3_prime_UTR_variant | 5/5 | ENST00000335765.9 | ||
UNC119 | NM_001330166.2 | c.*1C>T | 3_prime_UTR_variant | 6/6 | |||
UNC119 | NM_054035.2 | c.*328C>T | 3_prime_UTR_variant | 4/4 | |||
UNC119 | XM_011525459.3 | c.*507C>T | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC119 | ENST00000335765.9 | c.*1C>T | 3_prime_UTR_variant | 5/5 | 1 | NM_005148.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.126 AC: 19152AN: 152078Hom.: 1652 Cov.: 32
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GnomAD3 exomes AF: 0.131 AC: 32839AN: 251036Hom.: 2833 AF XY: 0.133 AC XY: 18030AN XY: 135728
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GnomAD4 exome AF: 0.159 AC: 232456AN: 1461658Hom.: 20433 Cov.: 33 AF XY: 0.157 AC XY: 114343AN XY: 727122
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GnomAD4 genome ? AF: 0.126 AC: 19152AN: 152196Hom.: 1652 Cov.: 32 AF XY: 0.123 AC XY: 9128AN XY: 74398
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
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 - |
Idiopathic CD4 lymphocytopenia Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Cone-rod dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
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DANN
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RBP_binding_hub_radar
RBP_regulation_power_radar
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