About PRPF8
No gene-level summary was recorded for this case.
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is benign. Select a step to read what it means.
Benign.A benign classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.No gene-level summary was recorded for this case.
The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
No pathogenic criterion marked as applied in the recorded assessment.
This variant has an allele frequency of 4.72% in the African/African American population in gnomAD v2.1 (1177/24962 alleles, 32 homozygotes) and 4.79% in gnomAD v4.1 (3597/75018 alleles, 85 homozygotes), far exceeding the 1% threshold for BA1. This population frequency is incompatible with a rare Mendelian disorder such as PRPF8-associated retinitis pigmentosa.
This variant has an overall allele frequency of 0.45% in gnomAD v2.1 (1280/282218 alleles) and 0.25% in gnomAD v4.1, exceeding the 0.3% BS1 threshold. This frequency is too high for a causative variant in PRPF8-associated retinitis pigmentosa. Note: BA1 (stand-alone benign) is also met based on the African subpopulation frequency; BS1 is met independently at the overall population level.
This variant has been observed in the homozygous state in 32 individuals in gnomAD v2.1 and 87 individuals in gnomAD v4.1. Observation in healthy homozygous adults is inconsistent with a fully penetrant dominant disorder such as PRPF8-associated retinitis pigmentosa.
SpliceAI predicts no splicing impact (max delta score = 0.00) for this intronic variant located 4 bases upstream of exon 43. Multiple in silico tools concordantly predict no deleterious effect.
ClinVar reports this variant as Benign from three independent clinical laboratories (Illumina, ARUP, and Labcorp/Invitae). While not meeting the 3-star expert panel threshold, the consensus among multiple clinical testing laboratories supports a benign interpretation.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BA1 stand-alone benign, BS1 strong benign, BS2 strong benign, BP4 supporting benign, BP6 supporting benign; combination = 1 stand-alone benign + 2 strong benign + 2 supporting benign, which maps to Benign.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 4,069 / 1,614,148 alleles. Recorded AF 0.00252083. Recorded homozygote count 87.
This variant is present in gnomAD v2.1 (AF= 0.0045355; MAF= 0.45355%, 1280/282218 alleles, homozygotes = 32) and has highest observed frequency in the African/African American population (AF= 0.0471517; MAF= 4.71517%, 1177/24962 alleles, homozygotes = 32); grpmax FAF= 0.0447737.
This variant is present in gnomAD-Canada v1.0 (AF= 0.002551851449668802, 47/18418 alleles, homozygotes = 0).
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
3 Benign. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
No standalone functional evidence summary is recorded in evidence_summary.functional.
This variant has not previously been reported in somatic cancers (COSMIC).
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
27 criteria with recorded statuses: 5 met · 16 not met · 0 not assessed · 6 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
NM_006445.3:c.6854-4G>A is classified as Benign.
This variant meets BA1 (stand-alone benign): allele frequency of 4.7% in the African/African American population in gnomAD (1177/24962 alleles, 32 homozygotes in v2.1; 3597/75018 alleles, 85 homozygotes in v4.1), far exceeding the 1% threshold and incompatible with a rare Mendelian disorder.
This variant also meets BS1 (strong benign) at the overall population level with an allele frequency of 0.45% in gnomAD v2.1, exceeding the 0.3% threshold.
This variant meets BS2 (strong benign): observed in 32 homozygous individuals in gnomAD v2.1 and 87 in v4.1, incompatible with a fully penetrant autosomal dominant retinal dystrophy.
SpliceAI predicts no splicing impact (max delta = 0.00), supporting BP4 (supporting benign).
ClinVar reports this variant as Benign from three independent clinical laboratories, supporting BP6 (supporting benign).
BA1 alone is sufficient for a Benign classification per the generic ACMG/AMP 2015 combination rules. Additional benign criteria (BS1, BS2, BP4, BP6) provide further confirmatory evidence.
No criteria match.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
Every interpreted variant in PRPF8, mapped onto the exon structure of NM_006445.3. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| African/African American3597 / 75,018 | 0.04885 hom |
| Middle Eastern20 / 6,060 | 0.0033 |
| Remaining individuals191 / 62,498 | 0.00312 hom |
| Admixed American173 / 60,026 | 0.0029 |
| South Asian19 / 91,082 | 0.00021 |
| East Asian6 / 44,882 | 0.00013 |
| European (non-Finnish)63 / 1,180,038 | 5.3e-05 |
| African/African American1177 / 24,962 | 0.04732 hom |
| Admixed American76 / 35,440 | 0.0021 |
| Remaining individuals10 / 7,224 | 0.0014 |
| South Asian5 / 30,616 | 0.00016 |
| East Asian3 / 19,952 | 0.00015 |
| European (non-Finnish)9 / 128,552 | 7e-05 |
This variant is present in gnomAD v4.1 (AF= 0.00252083; MAF= 0.25208%, 4069/1614148 alleles, homozygotes = 87) and has highest observed frequency in the African/African American population (AF= 0.0479485; MAF= 4.79485%, 3597/75018 alleles, homozygotes = 85); grpmax FAF= 0.0466408.
This variant is present in gnomAD v2.1 (AF= 0.0045355; MAF= 0.45355%, 1280/282218 alleles, homozygotes = 32) and has highest observed frequency in the African/African American population (AF= 0.0471517; MAF= 4.71517%, 1177/24962 alleles, homozygotes = 32); grpmax FAF= 0.0447737.
This variant is present in gnomAD-Canada v1.0 (AF= 0.002551851449668802, 47/18418 alleles, homozygotes = 0).
No further detail was recorded.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
5 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 0.00252083; MAF= 0.25208%, 4069/1614148 alleles, homozygotes = 87) and has highest observed frequency in the African/African American population (AF= 0.0479485; MAF= 4.79485%, 3597/75018 alleles, homozygotes = 85); grpmax FAF= 0.0466408.
This variant is present in gnomAD v2.1 (AF= 0.0045355; MAF= 0.45355%, 1280/282218 alleles, homozygotes = 32) and has highest observed frequency in the African/African American population (AF= 0.0471517; MAF= 4.71517%, 1177/24962 alleles, homozygotes = 32); grpmax FAF= 0.0447737.
This variant is present in gnomAD-Canada v1.0 (AF= 0.002551851449668802, 47/18418 alleles, homozygotes = 0).
This variant has been reported in ClinVar as Benign (3 clinical laboratories). (ClinVarID = 321870)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
This variant has not previously been reported in somatic cancers (COSMIC).