rs59977379
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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.322+142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0557 in 901,110 control chromosomes in the GnomAD database, including 1,580 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 0.052 ( 225 hom., cov: 32)
Exomes 𝑓: 0.056 ( 1355 hom. )
Consequence
PRPF31
NM_015629.4 intron
NM_015629.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.367
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=-0.94).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0605 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRPF31 | NM_015629.4 | c.322+142A>G | intron_variant | ENST00000321030.9 | |||
PRPF31-AS1 | XR_007067340.1 | n.1593T>C | non_coding_transcript_exon_variant | 2/3 | |||
PRPF31 | XM_006723137.5 | c.322+142A>G | intron_variant | ||||
PRPF31 | XM_047438587.1 | c.322+142A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRPF31 | ENST00000321030.9 | c.322+142A>G | intron_variant | 1 | NM_015629.4 | P1 | |||
PRPF31-AS1 | ENST00000452097.1 | n.3174T>C | non_coding_transcript_exon_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0521 AC: 7929AN: 152128Hom.: 223 Cov.: 32
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GnomAD4 exome AF: 0.0564 AC: 42263AN: 748864Hom.: 1355 Cov.: 10 AF XY: 0.0562 AC XY: 21910AN XY: 389716
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GnomAD4 genome ? AF: 0.0522 AC: 7941AN: 152246Hom.: 225 Cov.: 32 AF XY: 0.0521 AC XY: 3874AN XY: 74420
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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