BAP1 c.1120G>A, p.(Glu374Lys)

Reasoning

PM2 is met at supporting strength. NM_004656.4:c.1120G>A is absent from gnomAD v2.1 and gnomAD v4.1 all-comers datasets and from the available non-cancer subsets. This corresponds to an observed allele frequency of 0, meeting the supplied generic PM2 supporting threshold of <=0.0001. The variant is a missense substitution, so the indel population-calling caveat is not applicable.

Rule

PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868) ... Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v2.1 all-comers: NM_004656.4:c.1120G>A was absent.
• gnomAD v4.1 all-comers: NM_004656.4:c.1120G>A was absent.
• gnomAD v2.1 non-cancer and v3.1 non-cancer records also reported the variant as absent; no governing VCEP population-source override exists.
• Generic calibration threshold supplied for PM2 supporting: <=0.0001, identified as the SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020; PMID:25741868).

Sources

Reasoning

NM_004656.4:c.1120G>A is a missense variant producing NP_004647.1:p.(Glu374Lys), so the applicable generic PP3/BP4 path is REVEL only; the SpliceAI result is not used for a missense variant, and BayesDel has no established generic ACMG-strength calibration. REVEL is 0.202, which is at or below the generic BP4 supporting threshold of 0.29 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997), so BP4 is met at supporting strength.

Rule

Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only.

Evidence considered

• Variant consequence: missense, NM_004656.4:c.1120G>A, NP_004647.1:p.(Glu374Lys); therefore the generic missense REVEL path applies and the SpliceAI score is not used.
• Local REVEL lookup: score 0.202.
• Generic ClinGen SVI REVEL calibration: BP4 supporting requires <=0.29; threshold supplied in the governing case instructions and attributed to Pejaver et al. 2022, PMID:36413997.
• BayesDel score -0.131441 was not used because no generic ACMG-strength calibration is established for BayesDel.

Sources

Reasoning

NM_004656.4:c.1120G>A is a missense variant producing NP_004647.1:p.(Glu374Lys), so the applicable generic PP3/BP4 path is REVEL only; the SpliceAI result is not used for a missense variant, and BayesDel has no established generic ACMG-strength calibration. REVEL is 0.202, below the generic PP3 supporting threshold of 0.644 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997), so PP3 is not met.

Rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only.

Evidence considered

• Variant consequence: missense, NM_004656.4:c.1120G>A, NP_004647.1:p.(Glu374Lys); therefore the generic missense REVEL path applies and the SpliceAI score is not used.
• Local REVEL lookup: score 0.202.
• Generic ClinGen SVI REVEL calibration: PP3 supporting requires >=0.644; threshold supplied in the governing case instructions and attributed to Pejaver et al. 2022, PMID:36413997.
• BayesDel score -0.131441 was not used because no generic ACMG-strength calibration is established for BayesDel.

Sources

Reasoning

The exact variant NM_004656.4:c.1120G>A (p.Glu374Lys) is classified in ClinVar as Uncertain significance with criteria provided by single clinical laboratories. There is no ClinVar expert-panel classification and no exact-variant reputable-source Pathogenic or Likely pathogenic classification, so PP5 is not met.

Rule

Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 4194231 exactly matches NM_004656.4:c.1120G>A (p.Glu374Lys) and reports Uncertain significance with criteria provided by single submitters.
• The ClinVar submission audit reports 0 expert-panel submissions; the two submissions are clinical-laboratory submissions and neither is Pathogenic or Likely pathogenic.

Sources

Reasoning

BA1 is not met. NM_004656.4:c.1120G>A is absent from the default all-comers gnomAD v2.1 and gnomAD v4.1 datasets, as well as the available non-cancer subsets, so its observed allele frequency is 0 and does not reach the generic stand-alone BA1 threshold of >=0.05. The variant is a missense substitution; the indel-calling caveat does not apply.

Rule

BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868) ... Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v2.1 all-comers: NM_004656.4:c.1120G>A was absent.
• gnomAD v4.1 all-comers: NM_004656.4:c.1120G>A was absent.
• gnomAD v2.1 non-cancer and v3.1 non-cancer records also reported the variant as absent; no governing VCEP population-source override exists.
• Generic calibration threshold supplied for BA1: >= 0.05, identified as ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868).

Sources

Reasoning

BS1 is not met. The variant is absent from gnomAD v2.1 and gnomAD v4.1, with no observed population allele frequency exceeding the generic BS1 threshold of >=0.01. The available non-cancer subset records are also absent, and no disease-specific prevalence or penetrance calibration is supplied to support an alternative threshold.

Rule

BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168) ... Allele frequency is greater than expected for disorder.

Evidence considered

• gnomAD v2.1 all-comers: NM_004656.4:c.1120G>A was absent.
• gnomAD v4.1 all-comers: NM_004656.4:c.1120G>A was absent.
• gnomAD v2.1 non-cancer and v3.1 non-cancer records also reported the variant as absent; no governing VCEP population-source override exists.
• Generic calibration threshold supplied for BS1: >= 0.01, identified as the generic SVI default with per-gene derivation preferred (Whiffin et al. 2017, PMID:28518168).

Sources

Reasoning

The exact variant NM_004656.4:c.1120G>A (p.Glu374Lys) is classified in ClinVar as Uncertain significance with criteria provided by single clinical laboratories. There is no ClinVar expert-panel classification and no exact-variant reputable-source Benign or Likely benign classification, so BP6 is not met.

Rule

Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 4194231 exactly matches NM_004656.4:c.1120G>A (p.Glu374Lys) and reports Uncertain significance with criteria provided by single submitters.
• The ClinVar submission audit reports 0 expert-panel submissions; the two submissions are clinical-laboratory submissions and neither is Benign or Likely benign.

Sources

Reasoning

The variant is NP_004647.1:p.(Glu374Lys), but the available case evidence does not establish a previously pathogenic BAP1 variant producing the same amino-acid change at residue 374. The exact ClinVar record is classified as uncertain significance, and no qualifying same-amino-acid pathogenic comparator is documented. A definitive PS1 assessment would require an established pathogenic Glu374Lys variant, potentially from an alternate nucleotide change, with protein-level rather than splice-level evidence.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• The exact ClinVar record is NM_004656.4(BAP1):c.1120G>A (p.Glu374Lys), classified as uncertain significance with criteria provided by a single submitter; this is not an established pathogenic comparator.
• No same-amino-acid pathogenic comparator at BAP1 residue 374 is documented in the supplied literature and comparator evidence.

Still missing

• No qualifying previously established pathogenic variant with p.Glu374Lys was identified in the supplied evidence.

Sources

Reasoning

PS2 cannot be assessed because the available case evidence contains no proband-level disease documentation, parental testing results, confirmation of maternity and paternity, or family-history information establishing a de novo occurrence.

Rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.

Evidence considered

• The available case evidence provides no proband-level segregation or de novo testing data for NM_004656.4:c.1120G>A (BAP1 p.Glu374Lys).

Still missing

• Document the proband's disease phenotype and absence or presence of family history.
• Provide variant testing results for the biological mother and biological father, including confirmation of maternity and paternity.

Reasoning

No variant-specific in vitro or in vivo functional study was identified for BAP1 NM_004656.4:c.1120G>A (NP_004647.1:p.(Glu374Lys)). The reviewed literature consists of ACMG/AMP guidance and a cancer-predisposition referral guideline; neither reports an assay of this variant or provides validated, reproducible functional evidence supporting a damaging effect. PS3 therefore cannot be assessed.

Rule

PS3: Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Evidence considered

• The available literature review identified no report of a functional assay for NM_004656.4:c.1120G>A or NP_004647.1:p.(Glu374Lys).
• PMID:25741868 provides general ACMG/AMP interpretation guidance and does not mention BAP1 or this variant.
• PMID:25394175 is a general cancer-predisposition referral guideline and does not mention BAP1, this variant, or functional testing.

Still missing

• A variant-specific in vitro or in vivo assay addressing BAP1 protein function, activity, stability, localization, or biologically relevant cellular consequences is needed.
• Assay validation, appropriate controls, reproducibility, and biological relevance have not been documented.

Sources

Reasoning

No case-control study, affected-case prevalence, control prevalence, odds ratio, relative risk, or confidence interval for NM_004656.4:c.1120G>A was identified. The available literature entry PMID:25394175 is a general cancer-predisposition referral guideline and does not mention BAP1 or this variant; therefore the PS4 evidence requirement cannot be evaluated.

Rule

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.

Evidence considered

• PMID:25394175 was reviewed; it does not mention BAP1 or NM_004656.4:c.1120G>A and provides no case-control prevalence or effect estimate for this variant.
• No case-control cohort, affected-case series, odds ratio, relative risk, or confidence interval for the exact variant was present in the available evidence.

Still missing

• Variant-specific case-control data with affected and control counts or prevalence.
• Odds ratio or relative risk with a confidence interval.

Sources

Reasoning

The variant is p.Glu374Lys in BAP1. vcep_materials.json has no domain_tables entry for BAP1, and the supplied materials do not establish a qualifying mutational hotspot or a critical and well-established functional domain without benign variation. A domain-specific assessment remains open because no authoritative domain list or equivalent complete domain evidence is supplied.

Rule

Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.

Evidence considered

• vcep_materials.json reports an empty domain_tables object and no VCEP materials for BAP1.
• The supplied materials do not provide a complete, authoritative assessment of hotspot status or critical-domain benign variation for BAP1 residue 374.

Still missing

• No authoritative BAP1 domain table is present in vcep_materials.json.
• No complete domain-level assessment demonstrating a critical functional domain without benign variation is supplied.

Reasoning

The variant is p.Glu374Lys, but the supplied evidence does not document a different missense substitution at BAP1 residue 374 that has been determined to be pathogenic. The available exact ClinVar record is uncertain significance, and the PM5 candidate artifact contains no same-residue candidates. A qualifying pathogenic alternate missense at residue 374 is required for PM5.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

Evidence considered

• The exact p.Glu374Lys ClinVar record is classified as uncertain significance, not pathogenic.
• The PM5 candidate summary reports zero same-residue candidates and zero expert-panel or non-expert-majority pathogenic/likely pathogenic candidates.

Still missing

• No qualifying pathogenic alternate missense comparator at residue 374 is documented.

Sources

Reasoning

PM6 cannot be assessed because the available case evidence does not document an assumed de novo occurrence, a disease-affected proband, or parental testing that would show the variant is absent in the parents without confirmed maternity and paternity.

Rule

Assumed de novo, but without confirmation of paternity and maternity.

Evidence considered

• The available case evidence provides no parental testing, de novo assessment, or proband-level clinical data for NM_004656.4:c.1120G>A (BAP1 p.Glu374Lys).

Still missing

• Document the proband's disease phenotype.
• Provide testing results for both biological parents showing whether the variant is absent or present.
• Clarify whether maternity and paternity were confirmed.

Reasoning

PP1 cannot be assessed because the available case evidence contains no affected family members, variant-positive relatives, phenotype assessments, or meioses from which co-segregation could be evaluated.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• The available case evidence provides no family segregation data for NM_004656.4:c.1120G>A (BAP1 p.Glu374Lys).

Still missing

• Provide a pedigree identifying affected and unaffected relatives.
• Provide variant test results and reliable phenotype assessments for informative relatives.
• Report the number of informative meioses and whether the variant co-segregates with disease.

Reasoning

The supplied evidence does not establish both PP2 requirements for BAP1: a low rate of benign missense variation and missense variants as a common disease mechanism. Absence of this variant from gnomAD is variant-level rarity and does not establish the required gene-level benign-missense rate, while the available gene-level context does not provide a qualifying missense-mechanism assessment.

Rule

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Evidence considered

• The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, but these are observations about this variant and do not satisfy the gene-level PP2 requirements.
• The supplied case evidence does not provide a gene-level benign-missense-rate metric or a qualifying common-missense-mechanism determination for BAP1.

Still missing

• No gene-level analysis demonstrating a low rate of benign BAP1 missense variation is supplied.
• No gene-level evidence establishing missense variants as a common BAP1 disease mechanism is supplied.

Sources

Reasoning

The case evidence does not provide a patient phenotype or family history for the exact variant that can be assessed for high specificity to a disease with a single genetic etiology. The available PMID:25394175 paper is a general referral guideline and is not variant-specific.

Rule

Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• The available literature does not describe the phenotype or family history of the patient carrying NM_004656.4:c.1120G>A.
• PMID:25394175 was reviewed and does not mention BAP1 or this variant.

Still missing

• Patient phenotype and family-history details for this case.
• Evidence that the phenotype is highly specific for a disease with a single genetic etiology.

Sources

Reasoning

BS2 cannot be assessed from the available evidence. The case records contain population-database absence but do not document observation of NM_004656.4:c.1120G>A in a healthy adult as a homozygote, heterozygote, or hemizygote, nor do they establish the required full-penetrance early-age disease context.

Rule

Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.

Evidence considered

• The available gnomAD records report the variant as absent and therefore provide no healthy-carrier or homozygote observation for BS2.
• No case or population source in the reviewed evidence documents a healthy adult carrying this specific variant with the required zygosity.

Still missing

• A reliable healthy-adult observation is needed, including zygosity and confirmation that full penetrance is expected at an early age.

Reasoning

No variant-specific in vitro or in vivo functional study was identified for BAP1 NM_004656.4:c.1120G>A (NP_004647.1:p.(Glu374Lys)). The reviewed literature consists of ACMG/AMP guidance and a cancer-predisposition referral guideline; neither reports an assay of this variant or provides validated, reproducible functional evidence showing no damaging effect on protein function or splicing. BS3 therefore cannot be assessed.

Rule

BS3: Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.

Evidence considered

• The available literature review identified no report of a functional assay for NM_004656.4:c.1120G>A or NP_004647.1:p.(Glu374Lys).
• PMID:25741868 provides general ACMG/AMP interpretation guidance and does not mention BAP1 or this variant.
• PMID:25394175 is a general cancer-predisposition referral guideline and does not mention BAP1, this variant, or functional testing.

Still missing

• A variant-specific in vitro or in vivo assay addressing BAP1 protein function or splicing is needed.
• Assay validation, appropriate controls, reproducibility, and biological relevance have not been documented.

Sources

Reasoning

BS4 cannot be assessed because the available case evidence identifies no affected family members who were tested and found not to carry the variant; absence of segregation data is not evidence of lack of segregation.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• The available case evidence provides no tested affected relatives or non-segregation results for NM_004656.4:c.1120G>A (BAP1 p.Glu374Lys).

Still missing

• Provide a pedigree and identify affected relatives suitable for segregation analysis.
• Provide variant testing results for affected relatives.
• Assess possible phenocopies and the possibility of more than one pathogenic variant if non-segregation is observed.

Reasoning

The supplied evidence supports BAP1 loss-of-function as a disease mechanism but does not establish that primarily truncating variants, rather than missense variants, are known to cause disease. The available materials therefore do not satisfy the gene-level spectrum requirement for BP1, and no quantitative or comprehensive variant-class distribution is provided.

Rule

Missense variant in a gene for which primarily truncating variants are known to cause disease.

Evidence considered

• The gene-level context records BAP1 loss of function as a supported germline disease mechanism, but that does not by itself establish the BP1 requirement that primarily truncating variants are known to cause disease.
• No comprehensive or quantitative BAP1 variant-class evidence is supplied to determine whether truncating variants are the primary known disease mechanism relative to missense variants.

Still missing

• No comprehensive BAP1 disease-variant spectrum or gene-level evidence showing that primarily truncating variants cause disease is supplied.

Sources

Reasoning

BP2 requires either observation in trans with a pathogenic variant for a fully penetrant dominant disorder or observation in cis with a pathogenic variant in any inheritance pattern. Although the available BAP1 context describes an autosomal dominant syndrome, the case contains no documented pathogenic second variant, cis/trans phase result, parental or offspring testing, or affected-proband observation establishing either BP2 path.

Rule

BP2: Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.

Evidence considered

• pvs1_gene_context.json supporting-paper summary: BAP1 tumor predisposition syndrome is described as autosomal dominant.
• No pathogenic variant in cis or trans, phase testing, parental/offspring testing, or affected-proband allelic observation is documented for this variant.

Still missing

• Documented pathogenic second allele and its cis/trans phase relative to NM_004656.4:c.1120G>A.
• If applying the trans path, evidence that the dominant disorder is fully penetrant.

Sources

Reasoning

No report was identified showing this exact variant in a case with an alternate molecular basis for disease. The available exact-variant ClinVar submissions are uncertain-significance clinical-laboratory submissions and do not document an alternate molecular diagnosis; absence of such documentation is insufficient to establish that BP5 is not met.

Rule

Variant found in a case with an alternate molecular basis for disease.

Evidence considered

• ClinVar variation 4194231 contains two exact-variant clinical-laboratory submissions classified as Uncertain significance and does not document an alternate molecular basis for disease.
• No variant-specific case report with an alternate molecular diagnosis was identified in the reviewed evidence.

Still missing

• A case-level report linking the exact variant to an alternate molecular basis for disease.

Sources