chr1-150324880-C-CTTT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_004698.4(PRPF3):c.-48-5_-48-3dup variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.14 ( 1901 hom., cov: 0)
Exomes 𝑓: 0.36 ( 9793 hom. )
Failed GnomAD Quality Control
Consequence
PRPF3
NM_004698.4 splice_polypyrimidine_tract, intron
NM_004698.4 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.713
Genes affected
PRPF3 (HGNC:17348): (pre-mRNA processing factor 3) The removal of introns from nuclear pre-mRNAs occurs on complexes called spliceosomes, which are made up of 4 small nuclear ribonucleoprotein (snRNP) particles and an undefined number of transiently associated splicing factors. This gene product is one of several proteins that associate with U4 and U6 snRNPs. Mutations in this gene are associated with retinitis pigmentosa-18. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 1-150324880-C-CTTT is Benign according to our data. Variant chr1-150324880-C-CTTT is described in ClinVar as [Benign]. Clinvar id is 1178706.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRPF3 | NM_004698.4 | c.-48-5_-48-3dup | splice_polypyrimidine_tract_variant, intron_variant | ENST00000324862.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRPF3 | ENST00000324862.7 | c.-48-5_-48-3dup | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004698.4 | P1 | |||
PRPF3 | ENST00000496202.5 | n.115-5_115-3dup | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.144 AC: 20814AN: 144042Hom.: 1900 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.357 AC: 419749AN: 1176664Hom.: 9793 Cov.: 24 AF XY: 0.356 AC XY: 210468AN XY: 591106
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Data not reliable, filtered out with message: InbreedingCoeff
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GnomAD4 genome ? AF: 0.145 AC: 20818AN: 144068Hom.: 1901 Cov.: 0 AF XY: 0.145 AC XY: 10078AN XY: 69582
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 02, 2021 | - - |
Computational scores
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Name
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at