chr9-32540649-ATAAAG-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_005802.5(TOPORS):c.*733_*737del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0143 in 152,784 control chromosomes in the GnomAD database, including 24 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.014 ( 24 hom., cov: 32)
Exomes 𝑓: 0.037 ( 0 hom. )
Consequence
TOPORS
NM_005802.5 3_prime_UTR
NM_005802.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.531
Genes affected
TOPORS (HGNC:21653): (TOP1 binding arginine/serine rich protein, E3 ubiquitin ligase) This gene encodes a nuclear protein which is serine and arginine rich, and contains a RING-type zinc finger domain. It is highly expressed in the testis, and functions as an ubiquitin-protein E3 ligase. Mutations in this gene are associated with retinitis pigmentosa type 31. Alternatively spliced transcript variants, encoding different isoforms, have been observed for this locus. [provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 9-32540649-ATAAAG-A is Benign according to our data. Variant chr9-32540649-ATAAAG-A is described in ClinVar as [Likely_benign]. Clinvar id is 366548.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0142 (2164/152356) while in subpopulation NFE AF= 0.0203 (1381/68032). AF 95% confidence interval is 0.0194. There are 24 homozygotes in gnomad4. There are 1097 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2164 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOPORS | NM_005802.5 | c.*733_*737del | 3_prime_UTR_variant | 3/3 | ENST00000360538.7 | ||
TOPORS | NM_001195622.2 | c.*733_*737del | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOPORS | ENST00000360538.7 | c.*733_*737del | 3_prime_UTR_variant | 3/3 | 1 | NM_005802.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0142 AC: 2164AN: 152238Hom.: 24 Cov.: 32
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GnomAD4 exome AF: 0.0374 AC: 16AN: 428Hom.: 0 AF XY: 0.0433 AC XY: 11AN XY: 254
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Retinitis Pigmentosa, Dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at