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SF3B1Uncertain significance
Print report
Variant interpretation report

SF3B1

SF3B1 View identifiers
Classification
Uncertain significance

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.

Uncertain.The recorded classification is uncertain significance.

In plain language

Gene-level background from the recorded interpretation.

About the gene

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: 0
Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Uncertain significance

gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: none; combination = no applied criteria, which maps to VUS.

02The sources

Evidence at a glance

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

No screenshot for this evidence
Population frequency
Not recorded

gnomAD v4.1 allele counts were not recorded for this variant.

No listed criterion applied
No screenshot for this evidence
Computational predictions
Not recorded

No SpliceAI or REVEL score is recorded in the fields used for this tile.

No listed criterion applied
No screenshot for this evidence
ClinVar submissions
Not recorded

A ClinVar laboratory submission summary was not recorded.

Context only
No screenshot for this evidence
Functional evidence
Not recorded

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

No listed criterion applied
No screenshot for this evidence
Somatic evidence
Not assessed

No COSMIC evidence statement is recorded in this case.

Context only
For specialists

Technical detail

ACMG/AMP criteria under Not recorded, with the data and sources behind each one.

28 criteria with recorded statuses: 0 met · 0 not met · 28 not assessed · 0 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic
PVS1PS1PS2PS3PS4PM1PM2PM3PM4PM5PM6PP1PP2PP3PP4PP5
Benign
BA1BS1BS2BS3BS4BP1BP2BP3BP4BP5BP6BP7
Met Not met Not assessed Not applicable

A specific SF3B1 sequence change was not resolved, so this case could not be linked to variant-specific somatic observations or germline disease database entries.

Population evidence could not be assessed because no genomic coordinates or allele frequency data were available for comparison with ACMG/AMP frequency thresholds.

No variant-specific functional studies were identified, and generic PVS1 could not be applied because both the exact variant consequence and gene-level loss-of-function eligibility remained unresolved.

In silico evidence could not be assessed because no resolvable variant was available for SpliceAI, REVEL, BayesDel, or same-residue PM5 comparison.

Not assessed · 28 · no assessment recorded

PVS1 A specific sequence change, variant class, and transcript consequence were not resolved, and germline loss-of-function eligibility for this gene was not established. Available evidence therefore does not support applying generic PVS1 at this time. Details ▾Hide ▴
Evidence considered
  • Gene-level PVS1 gate remained manual-review required.
  • Variant-level PVS1 scaffold did not support generic PVS1 application.
Still missing
  • Resolve the exact variant nomenclature and consequence.
  • Establish whether germline loss of function is a validated disease mechanism for the relevant condition.
Sources
pvs1_gene_contextpvs1_variant_assessmentpvs1_generic_framework ↗PMC6185798
PS1 No specific nucleotide change or protein consequence was resolved, so it was not possible to determine whether this variant creates the same amino acid change as a previously established pathogenic variant. Details ▾Hide ▴
Still missing
  • Resolve the exact coding and protein change.
  • Compare the resolved amino acid substitution with established pathogenic variants.
PS2 No de novo data were identified for a specific variant, and no family-based confirmation could be evaluated. Details ▾Hide ▴
Still missing
  • Obtain the exact variant.
  • Review parental testing and phenotypic consistency if available.
PS3 No variant-specific functional studies were identified because a specific sequence change was not resolved and no relevant PMID-backed functional literature was retrieved. Details ▾Hide ▴
Evidence considered
  • No PMID-backed literature was retrieved.
Still missing
  • Resolve the exact variant.
  • Search for validated functional studies for that specific variant.
PS4 No variant-specific case enrichment or case-control data could be evaluated because a specific variant was not resolved. Details ▾Hide ▴
Still missing
  • Resolve the exact variant.
  • Review case counts
  • control counts
  • and any statistical enrichment data.
PM1 No amino acid position or protein domain could be assigned, so it was not possible to determine whether this variant lies in a critical region or mutational hot spot without benign variation. Details ▾Hide ▴
Still missing
  • Resolve the protein consequence and residue position.
  • Assess domain and hotspot context for the resolved variant.
PM2 No genomic coordinates were resolved, so no gnomAD population frequency was available. The PM2 threshold of less than 0.1% could therefore not be assessed. Details ▾Hide ▴
Still missing
  • Resolve genomic coordinates.
  • Review gnomAD v2.1 and v4.1 population frequencies for the exact variant.
PM3 No phase or trans observations with a pathogenic variant were identified, and no specific variant was available for recessive-case review. Details ▾Hide ▴
Still missing
  • Resolve the exact variant.
  • Review phase data and recessive case evidence if relevant.
PM4 No in-frame protein length change was established because the variant class and protein consequence were not resolved. Details ▾Hide ▴
Still missing
  • Resolve variant class and protein consequence.
  • Determine whether the resolved variant causes an in-frame insertion
  • deletion
  • or stop-loss.
PM5 Classic same-residue PM5 review could not be performed because no missense residue context was resolved, and available comparator harvesting did not confirm safe use of PM5 logic for this case. Details ▾Hide ▴
Evidence considered
  • No same-residue comparator candidates were established for adjudication.
Still missing
  • Resolve whether the variant is missense and identify the amino acid residue.
  • If missense
  • compare against established pathogenic or likely pathogenic variants at the same residue under the governing framework.
Sources
pm5_candidates
PM6 No assumed de novo evidence was identified for a specific variant, so PM6 could not be evaluated. Details ▾Hide ▴
Still missing
  • Resolve the exact variant.
  • Review parental status and phenotype data if available.
PP1 No segregation data were identified for a specific variant, so cosegregation with disease could not be assessed. Details ▾Hide ▴
Still missing
  • Resolve the exact variant.
  • Review informative family segregation data.
PP2 No resolved variant class was available, so it was not possible to determine whether this is a missense variant in a gene with low benign missense variation and a common pathogenic missense mechanism. Details ▾Hide ▴
Still missing
  • Resolve whether the variant is missense.
  • Confirm whether PP2 is appropriate for the relevant gene-disease context.
PP3 No computational predictor results were available because no specific variant coordinates or consequence were resolved. SpliceAI, REVEL, BayesDel, and HCI prior could not be assessed for this case. Details ▾Hide ▴
Evidence considered
  • No SpliceAI
  • REVEL
  • BayesDel
  • or HCI prior result was available for adjudication.
Still missing
  • Resolve the exact variant and genomic coordinates.
  • Review SpliceAI
  • REVEL
  • BayesDel
  • and any gene-specific computational framework for the resolved variant.
PP4 No phenotype-specific or molecularly specific disease presentation data were provided for a resolved variant, so PP4 could not be assessed. Details ▾Hide ▴
Still missing
  • Provide the relevant phenotype and clinical context.
  • Resolve the exact variant and assess phenotype specificity.
PP5 No resolved variant was available for review of reputable-source pathogenic assertions, and this criterion is not used without variant-specific supporting evidence. Details ▾Hide ▴
Still missing
  • Resolve the exact variant.
  • Review any reputable-source assertions only as allowed by the governing interpretation framework.
BA1 No gnomAD allele frequency was available because no genomic coordinates were resolved. The BA1 threshold of greater than 1% could therefore not be assessed. Details ▾Hide ▴
Still missing
  • Resolve genomic coordinates.
  • Review gnomAD v2.1 and v4.1 allele frequencies for the exact variant.
BS1 No gnomAD allele frequency was available because no genomic coordinates were resolved. The BS1 threshold of greater than 0.3% could therefore not be assessed. Details ▾Hide ▴
Still missing
  • Resolve genomic coordinates.
  • Review gnomAD v2.1 and v4.1 allele frequencies for the exact variant.
BS2 No specific variant was resolved, so observation in healthy adult individuals could not be evaluated. Details ▾Hide ▴
Still missing
  • Resolve the exact variant.
  • Review population and cohort observations in unaffected individuals if relevant.
BS3 No well-established functional studies showing a benign effect were identified because a specific variant was not resolved and no relevant PMID-backed functional literature was retrieved. Details ▾Hide ▴
Evidence considered
  • No PMID-backed literature was retrieved.
Still missing
  • Resolve the exact variant.
  • Search for validated functional studies showing no damaging effect for that variant.
BS4 No family segregation data were identified for a specific variant, so lack of segregation with disease could not be assessed. Details ▾Hide ▴
Still missing
  • Resolve the exact variant.
  • Review informative pedigree data if available.
BP1 No resolved variant class was available, so it could not be determined whether this is a missense change in a gene where truncating variants are the predominant established disease mechanism. Details ▾Hide ▴
Still missing
  • Resolve variant class and gene-disease mechanism.
BP2 No phase data were identified, so it was not possible to determine whether this variant is observed in trans with a pathogenic variant for a dominant disorder or in cis for any disorder. Details ▾Hide ▴
Still missing
  • Resolve the exact variant.
  • Review phase information and inheritance context.
BP3 No in-frame deletion or insertion within a repetitive region without known function was established because the variant class and location were not resolved. Details ▾Hide ▴
Still missing
  • Resolve variant class and protein consequence.
BP4 No computational predictor results were available because no specific variant coordinates or consequence were resolved. SpliceAI, REVEL, BayesDel, and HCI prior could not be used to support a benign interpretation. Details ▾Hide ▴
Evidence considered
  • No SpliceAI
  • REVEL
  • BayesDel
  • or HCI prior result was available for adjudication.
Still missing
  • Resolve the exact variant and genomic coordinates.
  • Review SpliceAI
  • REVEL
  • BayesDel
  • and any gene-specific computational framework for the resolved variant.
BP5 No alternate molecular explanation or resolved variant-specific clinical context was provided, so BP5 could not be assessed. Details ▾Hide ▴
Still missing
  • Provide phenotype and alternate diagnostic findings if relevant.
  • Resolve the exact variant.
BP6 No resolved variant was available for review of reputable-source benign assertions, and this criterion is not used without variant-specific supporting evidence. Details ▾Hide ▴
Still missing
  • Resolve the exact variant.
  • Review any reputable-source assertions only as allowed by the governing interpretation framework.
BP7 No synonymous or intronic variant context was resolved, and no splice prediction data were available, so BP7 could not be assessed. Details ▾Hide ▴
Still missing
  • Resolve the exact variant class and location.
  • Review splice prediction data if the resolved variant is synonymous or near splice-relevant intronic positions.

Identifiers

Coding (HGVS c.)
SF3B1
gnomAD v4.1 Allele count data not recorded
gnomAD v2.1 Allele count data not recorded

Statements

No population statements were recorded.

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

PP3 No computational predictor results were available because no specific variant coordinates or consequence were resolved. SpliceAI, REVEL, BayesDel, and HCI prior could not be assessed for this case. Details ▾Hide ▴
Evidence considered
  • No SpliceAI
  • REVEL
  • BayesDel
  • or HCI prior result was available for adjudication.
Still missing
  • Resolve the exact variant and genomic coordinates.
  • Review SpliceAI
  • REVEL
  • BayesDel
  • and any gene-specific computational framework for the resolved variant.
BP4 No computational predictor results were available because no specific variant coordinates or consequence were resolved. SpliceAI, REVEL, BayesDel, and HCI prior could not be used to support a benign interpretation. Details ▾Hide ▴
Evidence considered
  • No SpliceAI
  • REVEL
  • BayesDel
  • or HCI prior result was available for adjudication.
Still missing
  • Resolve the exact variant and genomic coordinates.
  • Review SpliceAI
  • REVEL
  • BayesDel
  • and any gene-specific computational framework for the resolved variant.
BP7 No synonymous or intronic variant context was resolved, and no splice prediction data were available, so BP7 could not be assessed. Details ▾Hide ▴
Still missing
  • Resolve the exact variant class and location.
  • Review splice prediction data if the resolved variant is synonymous or near splice-relevant intronic positions.

0 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.