rs56220912
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015629.4(PRPF31):c.420+82G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 1,110,294 control chromosomes in the GnomAD database, including 360,973 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.82 ( 51147 hom., cov: 31)
Exomes 𝑓: 0.80 ( 309826 hom. )
Consequence
PRPF31
NM_015629.4 intron
NM_015629.4 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.861
Genes affected
PRPF31 (HGNC:15446): (pre-mRNA processing factor 31) This gene encodes a component of the spliceosome complex and is one of several retinitis pigmentosa-causing genes. When the gene product is added to the spliceosome complex, activation occurs.[provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRPF31 | NM_015629.4 | c.420+82G>C | intron_variant | ENST00000321030.9 | |||
PRPF31-AS1 | XR_007067340.1 | n.1002C>G | non_coding_transcript_exon_variant | 2/3 | |||
PRPF31 | XM_006723137.5 | c.420+82G>C | intron_variant | ||||
PRPF31 | XM_047438587.1 | c.420+82G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRPF31 | ENST00000321030.9 | c.420+82G>C | intron_variant | 1 | NM_015629.4 | P1 | |||
PRPF31-AS1 | ENST00000452097.1 | n.2668C>G | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.819 AC: 124462AN: 151950Hom.: 51092 Cov.: 31
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GnomAD4 exome AF: 0.804 AC: 770006AN: 958226Hom.: 309826 Cov.: 13 AF XY: 0.803 AC XY: 400161AN XY: 498028
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GnomAD4 genome ? AF: 0.819 AC: 124575AN: 152068Hom.: 51147 Cov.: 31 AF XY: 0.815 AC XY: 60574AN XY: 74328
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at