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Variant interpretation report

PRPF8 c.6854-4G>A, p.?

NM_006445.3:c.6854-4G>A NP_006436.3:p.? View identifiers
Classification
Benign

Variant description:

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.

In plain language

Gene-level background from the recorded interpretation.

About PRPF8

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 0 Benign evidence criteria: 5
Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 5
BA1Stand alone
BA1 · stand alone

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.

BS1Strong
BS1 · strong

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.

BS2Strong
BS2 · strong

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.

BP4Supporting
BP4 · supporting

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.

BP6Supporting
BP6 · supporting

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.

Recorded classification: Benign

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.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1
gnomAD v2.1
Population frequency
4,069 / 1,614,148 alleles

gnomAD v4.1: 4,069 / 1,614,148 alleles. Recorded AF 0.00252083. Recorded homozygote count 87.

gnomAD v2.1

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.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.002551851449668802, 47/18418 alleles, homozygotes = 0).

SpliceAI score
0.000 maximum delta

Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.

ClinVar submissions
3 reported laboratory submissions

3 Benign. ClinVar API review status: criteria provided, multiple submitters, no conflicts.

No screenshot for this evidence
Functional evidence
Not recorded

No standalone functional evidence summary is recorded in evidence_summary.functional.

No listed criterion applied OncoKB ↗
Somatic evidence
No matching record reported

This variant has not previously been reported in somatic cancers (COSMIC).

Context only COSMIC ↗
For specialists

Technical detail

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.

Met Not met Not assessed Not applicable

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.

Met · 5

BA1 Stand aloneThis 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. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1 African/African American AF = 4.72% (1177/24962 alleles
  • 32 homozygotes)
  • gnomAD v4.1 African/African American AF = 4.79% (3597/75018 alleles
  • 85 homozygotes)
  • grpmax FAF v2.1 = 0.0448
  • v4.1 = 0.0466
  • Far exceeds 1% BA1 threshold defined for generic ACMG non-VCEP adjudication
Sources
BS1 StrongThis 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. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1 overall AF = 0.45% (1280/282218 alleles)
  • gnomAD v4.1 overall AF = 0.25% (4069/1614148 alleles)
  • Exceeds 0.3% BS1 threshold defined for generic ACMG non-VCEP adjudication
Sources
BS2 StrongThis 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. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1: 32 homozygotes observed
  • gnomAD v4.1: 87 homozygotes observed
  • Homozygous state incompatible with a fully penetrant autosomal dominant retinal dystrophy
Sources
BP4 SupportingSpliceAI 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. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta = 0.00 — no predicted donor/acceptor gain or loss
  • Located at c.6854-4
  • outside the canonical splice consensus
  • with no predicted splicing alteration
Sources
BP6 SupportingClinVar 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. Details ▾Hide ▴
Evidence considered
  • ClinVar Variation ID: 321870
  • classification: Benign
  • 3 clinical laboratories concur (Illumina
  • ARUP
  • Labcorp/Invitae)
  • Review status: criteria provided
  • single submitter (1-star)
Sources

Not met · 16 · evaluated, threshold not reached

PVS1 NM_006445.3:c.6854-4G>A is an intronic variant located 4 bases upstream of exon 43. It does not affect the canonical splice consensus (±1,2), SpliceAI predicts no splicing impact (max delta = 0.00), and the variant does not fall into a default PVS1 null-variant bucket. The generic PVS1 framework does not apply. Details ▾Hide ▴
Evidence considered
  • Intronic variant at c.6854-4
  • outside canonical ±1
  • 2 splice consensus
  • SpliceAI max delta score = 0.00
  • no predicted splicing impact
  • Variant bucket = 'other' per PVS1 variant assessment
  • generic PVS1 framework not applicable
Sources
PS2 No de novo observation has been reported for NM_006445.3:c.6854-4G>A in any reviewed publication or database submission. Details ▾Hide ▴
Still missing
  • No de novo data available
PS3 No functional data exists for NM_006445.3:c.6854-4G>A or a systematically characterized range that includes this variant. The variant has not been directly tested in any experimental assay, and no publication reviewed contains functional evidence for this intronic substitution. Details ▾Hide ▴
Evidence considered
  • No variant-specific functional studies identified in literature
  • SpliceAI max delta = 0.00 indicates no predicted splicing defect
  • but this is in silico prediction
  • not experimental functional evidence
Still missing
  • No experimental functional data available for this variant
PS4 This variant is common in population databases (gnomAD overall AF = 0.45%, African AF = 4.7%), which is incompatible with the prevalence of PRPF8-associated retinitis pigmentosa. No case-control enrichment in affected individuals has been demonstrated. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1: 1280/282218 alleles (0.45%)
  • 32 homozygotes
  • gnomAD v4.1: 4069/1614148 alleles (0.25%)
  • 87 homozygotes
  • African/African American AF = 4.7% (v2.1)
  • far too common for a rare Mendelian disease
Sources
PM1 Located in a region with substantial benign variation in population databases (AF = 4.7% in African population, 32 homozygotes in gnomAD). A mutational hotspot or critical functional domain cannot be invoked when the region tolerates high-frequency benign variation. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1: 32 homozygotes
  • AF = 4.7% in African population
  • High frequency of benign variation at this locus precludes PM1 application
Sources
PM2 This variant is present in gnomAD at an overall allele frequency of 0.45%, far above the 0.1% threshold for PM2 in the generic ACMG framework. It is a common polymorphism, not a rare variant absent from population databases. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1 AF = 0.45% (1280/282218 alleles)
  • gnomAD v4.1 AF = 0.25% (4069/1614148 alleles)
  • Well above PM2 threshold of <0.1%
Sources
PM6 No de novo observation has been reported for this variant in any reviewed source. PM6 requires a confirmed de novo occurrence with or without paternity/maternity confirmation. Details ▾Hide ▴
Still missing
  • No de novo data available
PP1 No cosegregation data has been reported for NM_006445.3:c.6854-4G>A in any family. No publication or ClinVar submission contains segregation analysis for this variant. Details ▾Hide ▴
Still missing
  • No cosegregation data available
PP3 Multiple lines of in silico evidence predict no pathogenic effect. SpliceAI predicts no splicing impact (max delta = 0.00). REVEL and BayesDel scores are not available for this intronic variant. No computational tool supports a deleterious effect. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta = 0.00 (no predicted splice alteration)
  • REVEL and BayesDel not computed for intronic variants
Sources
PP4 No patient phenotype data specific to this variant has been reported. PP4 requires that the variant be identified in a patient whose phenotype is highly specific for the gene/disease. Details ▾Hide ▴
Still missing
  • No patient phenotype data available
PP5 ClinVar classifies this variant as Benign (3 clinical laboratories). No reputable source has reported it as pathogenic. PP5 requires a reputable source to report the variant as pathogenic with unavailable supporting evidence. Details ▾Hide ▴
Evidence considered
  • ClinVar classification: Benign (Variation ID: 321870)
  • Review status: criteria provided
  • single submitter (1-star)
Sources
BS3 No well-established in vitro or in vivo functional study has directly assessed the effect of NM_006445.3:c.6854-4G>A. While SpliceAI predicts no splicing impact (max delta = 0.00), this is in silico evidence (BP4), not experimental functional data required for BS3. Details ▾Hide ▴
Evidence considered
  • No experimental functional studies of this variant identified
Still missing
  • No experimental functional data available
BS4 No nonsegregation data has been reported for this variant. BS4 requires the variant to be observed in trans or to fail to segregate with disease in affected families. Details ▾Hide ▴
Still missing
  • No nonsegregation data available
BP2 No observation of this variant in trans with a known pathogenic PRPF8 variant has been reported. BP2 requires the variant to be observed in cis or in trans with a pathogenic variant in a recessive disorder, or in trans with a pathogenic variant for a fully penetrant dominant disorder. Details ▾Hide ▴
Still missing
  • No phase data available
BP5 No case has been reported where NM_006445.3:c.6854-4G>A was found in a patient with an alternative molecular basis for disease. BP5 requires the variant to be observed in a case with an alternate established pathogenic cause. Details ▾Hide ▴
Still missing
  • No alternate molecular cause data available
PS5 ClinVar classifies this variant as Benign, not Pathogenic. No reputable source has reported this variant as pathogenic. Details ▾Hide ▴
Evidence considered
  • ClinVar classification: Benign (Variation ID: 321870)
  • 3 clinical laboratories concur on Benign classification
Sources
Not applicable · 6· recorded as not applicable Show reasons ▾Hide reasons ▴
PS1 N/AIntronic variant with no predicted protein change; PS1 applies only to variants producing the same amino acid change as an established pathogenic variant. Details ▾Hide ▴

No further detail was recorded.

PM5 N/AIntronic variant with no predicted amino acid residue; PM5 requires a different pathogenic missense change at the same residue, which is not applicable for non-coding variants. Details ▾Hide ▴
Sources
pm5_candidates
PP2 N/APP2 applies to missense variants in genes with a low rate of benign missense variation. This is an intronic substitution, not a missense variant. Details ▾Hide ▴

No further detail was recorded.

BP1 N/ABP1 applies to missense variants in genes where only truncating variants cause disease. This is an intronic substitution, not a missense variant. Details ▾Hide ▴

No further detail was recorded.

BP3 N/ASkipped per instruction. This is a substitution variant, not an in-frame indel in a repetitive region. Details ▾Hide ▴

No further detail was recorded.

BP7 N/ABP7 applies to synonymous variants with no predicted splice impact. This is an intronic variant (c.6854-4G>A), not a synonymous coding variant. Details ▾Hide ▴

No further detail was recorded.

Identifiers

Gene
PRPF8
Transcript
NM_006445.3
Coding (HGVS c.)
NM_006445.3:c.6854-4G>A
Protein (HGVS p.)
NP_006436.3:p.?
GRCh38
chr17:1650960 C>T
GRCh37
chr17:1554254 C>T
ClinVar
321870

Gene diagram

Every interpreted variant in PRPF8, mapped onto the exon structure of NM_006445.3. Select a row to find it on the plot.

PRPF8NM_006445.3
Fetching transcript structure from UCSC…
gnomAD v4.1 4,069 / 1,614,148 alleles AF 0.00252 · 87 homozygotes · FAF 0.0466
gnomAD v2.1 1,280 / 282,218 alleles AF 0.00454 · 32 homozygotes · FAF 0.0448
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 0.0025 · 4069 / 1,614,148 alleles · 87 hom · FAF 0.047
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
0 alternate alleles recorded in 3 other groups: European (Finnish), Amish, Ashkenazi Jewish.

gnomAD v2.1

AF 0.0045 · 1280 / 282,218 alleles · 32 hom · FAF 0.045
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
0 alternate alleles recorded in 2 other groups: Ashkenazi Jewish, European (Finnish).

gnomAD-Canada

AF not recorded · ? / ? alleles

Statements

gnomAD v4.1

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.

gnomAD v2.1

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.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.002551851449668802, 47/18418 alleles, homozygotes = 0).

Open the gnomAD-Canada detail page →

SpliceAI and Pangolin

Pangolin splice lossmagnitude shown
-0.020
Pangolin splice gain
0.010

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

BP4 SupportingSpliceAI 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. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta = 0.00 — no predicted donor/acceptor gain or loss
  • Located at c.6854-4
  • outside the canonical splice consensus
  • with no predicted splicing alteration
Sources
PP3 Multiple lines of in silico evidence predict no pathogenic effect. SpliceAI predicts no splicing impact (max delta = 0.00). REVEL and BayesDel scores are not available for this intronic variant. No computational tool supports a deleterious effect. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta = 0.00 (no predicted splice alteration)
  • REVEL and BayesDel not computed for intronic variants
Sources
BP7 N/ABP7 applies to synonymous variants with no predicted splice impact. This is an intronic variant (c.6854-4G>A), not a synonymous coding variant. Details ▾Hide ▴

No further detail was recorded.

Statement

In silico

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.

Recorded publications

  • Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
    Richards S et al. · 2015
    Standards and guidelines for the interpretation of sequence variants (ACMG/AMP 2015). This paper defines the generic ACMG/AMP classification framework used for this adjudication. NM_006445.3:c.6854-4G>A is not mentioned.
    Does not name this variant
    PMID 25741868 ↗
  • In Vivo CRISPR/Cas9 Gene Editing Corrects Retinal Dystrophy in the S334ter-3 Rat Model of Autosomal Dominant Retinitis Pigmentosa.
    Bakondi B et al. · 2016
    Reports in vivo CRISPR/Cas9 gene editing to correct retinal dystrophy in the S334ter rat model of autosomal dominant retinitis pigmentosa caused by RHO mutations. This study concerns the rhodopsin (RHO) gene, not PRPF8. NM_006445.3:c.6854-4G>A is not mentioned.
    Does not name this variant
    PMID 26666451 ↗
  • Nonsyndromic Retinitis Pigmentosa Overview.
    Adam MP et al. · 1993
    GeneReviews overview of nonsyndromic retinitis pigmentosa. This is a clinical summary of RP genes including PRPF8. The specific variant NM_006445.3:c.6854-4G>A was not identified in the available metadata; full text was not available for direct confirmation.
    Does not name this variant
    PMID 20301590 ↗
  • Clinical utility gene card for: BEST1-related dystrophies (Bestrophinopathies).
    Ramsden SC et al. · 2012
    Clinical utility gene card for BEST1-related dystrophies (bestrophinopathies). This paper discusses BEST1 mutations and phenotypes. PRPF8 and NM_006445.3:c.6854-4G>A are not mentioned — the paper concerns a different gene entirely.
    Does not name this variant
    PMID 22234150 ↗
  • Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
    Nykamp K et al. · 2017
    Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. A framework methodology paper describing variant classification refinements. NM_006445.3:c.6854-4G>A is not mentioned.
    Does not name this variant
    PMID 28492532 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

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.

gnomAD v2.1

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.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.002551851449668802, 47/18418 alleles, homozygotes = 0).

ClinVar

This variant has been reported in ClinVar as Benign (3 clinical laboratories). (ClinVarID = 321870)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).

Somatic

This variant has not previously been reported in somatic cancers (COSMIC).