BAP1 c.121G>A, p.(Gly41Ser)

Reasoning

BS4 supports benign interpretation when a variant fails to segregate with disease in affected family members. For the exact BAP1 c.121G>A (p.G41S) variant, the family included two first-degree and one second-degree relatives with renal cell carcinoma, and the paper states that cosegregation studies suggested the variant was not responsible for the family's cancer predisposition. This is direct non-segregation evidence supporting BS4 at supporting strength, although the detailed family genotypes are not reproduced in the main text.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family; apply at supporting strength here because the publication reports discordant cosegregation but the detailed pedigree genotypes require human confirmation.

Evidence considered

• PMID:23709298 reports the exact variant in individual II:1 in a family with two first-degree and one second-degree relatives with renal cell carcinoma.
• PMID:23709298 states that cosegregation studies suggested the variant was not responsible for the family's cancer predisposition, which is consistent with lack of segregation in affected relatives and supports BS4.

Still missing

• Detailed genotypes, affection status, and the exact number of informative meioses are not provided in the extracted main-text passage; review Supplementary Figure S1 for final clinical sign-off.

Sources

Reasoning

BP4 is applicable because NM_004656.4:c.121G>A is a missense variant, NP_004647.1:p.(Gly41Ser). The calibrated missense predictor result, REVEL 0.072, meets the generic BP4 supporting threshold of <=0.29 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997). The independent splice-impact path is also concordant: SpliceAI max delta 0.009 meets the generic BP4 supporting threshold of <=0.1 from the SpliceAI recommended cutoff (Jaganathan et al. 2019, PMID:30661751). These predictor results are used once for BP4 and are not duplicated as pathogenic evidence for PP3. BayesDel is not used because no generic ACMG-strength calibration is established and no governing VCEP cutoff is available. The concordant calibrated results support BP4 at supporting strength, without escalation beyond supporting.

Rule

generic_calibrated_computational_evidence: missense; BP4 supporting requires REVEL <=0.29 or SpliceAI max delta <=0.1; BayesDel requires a VCEP-specific cutoff

Evidence considered

• Variant scope: NM_004656.4:c.121G>A is a missense substitution producing NP_004647.1:p.(Gly41Ser), so BP4 is applicable.
• REVEL score 0.072 meets the generic BP4 supporting threshold of <=0.29; threshold from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997).
• SpliceAI max delta 0.009 meets the generic BP4 supporting threshold of <=0.1; threshold from the SpliceAI recommended cutoff (Jaganathan et al. 2019, PMID:30661751).
• BayesDel score -0.479536 was not used because no generic ACMG-strength calibration is established and no governing VCEP cutoff is available.

Sources

Reasoning

PS1 requires a previously established pathogenic variant producing the same amino-acid change. The exact variant p.Gly41Ser is reported in the literature and ClinVar as benign/probably benign, and no independent pathogenic assertion for the same amino-acid change is present. Therefore PS1 is not met.

Rule

PS1: same amino-acid change as a previously established pathogenic variant; an exact pathogenic same-change comparator is required.

Evidence considered

• ClinVar variation 133667 identifies NM_004656.4:c.121G>A (p.Gly41Ser) and summarizes six benign and five likely-benign laboratory submissions.
• The exact p.Gly41Ser variant was reported in a germline RCC-predisposition evaluation, but cosegregation suggested it was not responsible for the family's cancer predisposition.
• A review lists the exact G121A (Gly41Ser) variant as probably benign in its germline BAP1 mutation table.

Sources

Reasoning

Generic ACMG/AMP PS4 requires a statistically significant enrichment of the exact variant in affected individuals compared with an appropriate control population. The literature documents the exact BAP1 c.121G>A (p.Gly41Ser) variant in one individual from a family with two first-degree and one second-degree relatives with renal cell carcinoma, but cosegregation studies reported that the variant was not responsible for the family's cancer predisposition. No case-control enrichment, odds ratio, or statistically significant prevalence estimate is available. Therefore, the available exact-variant clinical observation does not meet PS4 and includes evidence against disease association.

Rule

Generic ACMG/AMP PS4: prevalence of the disease-causing variant in affected individuals is significantly increased compared with controls; no exact-variant case-control enrichment statistic is available, and reported cosegregation argues against association.

Evidence considered

• PMID:23709298 reports the exact c.121G>A (p.G41S) variant in one individual from a family with two first-degree and one second-degree relatives with renal cell carcinoma, but states that cosegregation studies suggested the variant was not responsible for the cancer predisposition.
• PMID:22683710 independently reports the exact c.121G>A (p.Gly41Ser) germline variant in one individual with relatives affected by renal cell carcinoma, without a case-control enrichment analysis.
• PMID:26166446 summarizes the exact Gly41Ser germline variant in one individual with renal cell carcinoma family history and lists it as probably benign; this is contextual evidence, not a substitute for PS4 enrichment.

Still missing

• No case-control comparison of exact-variant prevalence in affected individuals versus controls.
• No odds ratio, p-value, or other validated enrichment statistic for this exact variant.

Sources

Reasoning

No governing BAP1 VCEP or gene-specific framework was available, so the supplied generic PM2 threshold of <=0.0001 was used. The variant is present at AF 0.0007069985789328563 in gnomAD v2.1 and 0.0003679932596520791 in gnomAD v4.1, with 200 and 594 observed alleles, respectively. Both all-comers frequencies exceed 0.0001, so the variant does not meet generic PM2. The non-cancer subset frequencies are also above this threshold in gnomAD v2.1 (0.0008271508030959073) and gnomAD v3.1 (0.00020958124315480618).

Rule

Generic ACMG PM2 Supporting: allele frequency <=0.0001; no applicable BAP1-specific specification was available.

Evidence considered

• No applicable BAP1 VCEP or gene-specific framework was available; the supplied generic ACMG PM2 threshold of <=0.0001 was applied.
• gnomAD v2.1 all-comers reports AF 0.0007069985789328563 from 200/282886 alleles; gnomAD v4.1 all-comers reports AF 0.0003679932596520791 from 594/1614160 alleles.
• For completeness, the available non-cancer records also exceed the generic threshold: gnomAD v2.1 non-cancer exomes AF 0.0008271508030959073 from 196/236958 alleles, and gnomAD v3.1 non-cancer genomes AF 0.00020958124315480618 from 31/147914 alleles.

Sources

Reasoning

PM5 requires a different missense change at the same residue that is established as pathogenic. The available same-residue search artifact contains no comparator variants, and the reviewed literature identifies Gly41Ser itself but no pathogenic alternate substitution at Gly41. The reported Leu14His variant is at residue 14, not residue 41, and cannot satisfy PM5.

Rule

PM5: novel missense change at an amino-acid residue where a different missense change is established as pathogenic.

Evidence considered

• The same-residue comparator artifact reports zero collected candidates and no confirmed PM5 comparator.
• The literature reports Gly41Ser itself, not a pathogenic alternate substitution at Gly41.
• The review discusses Leu14His as a distinct variant at residue 14 and therefore it is not a same-residue PM5 comparator.

Sources

Reasoning

PP1 requires cosegregation of the variant with disease in affected family members. In the family containing the exact c.121G>A (p.Gly41Ser) variant, two first-degree and one second-degree relatives had renal cell carcinoma, but the published cosegregation studies suggested that the variant was not responsible for the family's cancer predisposition. This is contrary to positive disease segregation, so PP1 is not met.

Rule

Generic ACMG/AMP PP1: cosegregation with disease in affected family members; the reported negative/discordant cosegregation conclusion does not satisfy PP1.

Evidence considered

• PMID:23709298 reports the exact variant in individual II:1 from a family with two first-degree and one second-degree relatives with renal cell carcinoma.
• PMID:23709298 explicitly states that cosegregation studies suggested c.121G>A (p.G41S) was not responsible for the family's cancer predisposition, providing no positive segregation support for PP1.

Still missing

• The publication does not provide the individual genotypes and phenotype status for every tested family member in the main text.

Sources

Reasoning

PP3 is applicable because NM_004656.4:c.121G>A is a missense variant, NP_004647.1:p.(Gly41Ser). The calibrated missense predictor result is REVEL 0.072, below the generic PP3 supporting threshold of >=0.644 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997). The splice-impact result is SpliceAI max delta 0.009, below the generic PP3 supporting threshold of >=0.2 from the SpliceAI recommended cutoff (Jaganathan et al. 2019, PMID:30661751). BayesDel is not interpretable for PP3 because no generic ACMG-strength calibration is established and no governing VCEP cutoff is available. Therefore, no calibrated computational evidence supports a pathogenic prediction for PP3.

Rule

generic_calibrated_computational_evidence: missense; PP3 supporting requires REVEL >=0.644 or SpliceAI max delta >=0.2; BayesDel requires a VCEP-specific cutoff

Evidence considered

• Variant scope: NM_004656.4:c.121G>A is a missense substitution producing NP_004647.1:p.(Gly41Ser), so PP3 is applicable.
• REVEL score 0.072 does not meet the generic PP3 supporting threshold of >=0.644; threshold from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997).
• SpliceAI max delta 0.009 does not meet the generic PP3 supporting threshold of >=0.2; threshold from the SpliceAI recommended cutoff (Jaganathan et al. 2019, PMID:30661751).
• BayesDel score -0.479536 was not used because no generic ACMG-strength calibration is established and no governing VCEP cutoff is available.

Sources

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. ClinVar exactly matches NM_004656.4:c.121G>A (p.Gly41Ser), but the record has no expert-panel submissions and contains only ordinary laboratory submissions, with Benign and Likely benign classifications. PP5 is therefore not met.

Rule

PP5: apply only when an exact-variant ClinVar expert panel classifies the variant as Pathogenic or Likely pathogenic; ordinary submissions and aggregate labels do not qualify.

Evidence considered

• ClinVar exact-match record NM_004656.4(BAP1):c.121G>A (p.Gly41Ser) reports zero expert-panel submissions and ordinary laboratory classifications of Benign or Likely benign.

Still missing

• No exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Sources

Reasoning

No governing BAP1 VCEP or gene-specific framework was available, so the supplied generic BA1 threshold of >=0.05 was used. gnomAD v4.1 reports the highest observed population frequency in South Asians at 0.004325392468986717 (grpmax FAF 0.00397315), and gnomAD v2.1 reports 0.004442121766396656 (grpmax FAF 0.00383396); both are below 0.05. The lower combined all-comers frequencies are also far below the threshold.

Rule

Generic ACMG BA1: allele frequency >=0.05; no applicable BAP1-specific specification was available.

Evidence considered

• No applicable BAP1 VCEP or gene-specific framework was available; the supplied generic ACMG BA1 threshold of >=0.05 was applied.
• gnomAD v2.1 reports highest South Asian AF 0.004442121766396656 and grpmax FAF 0.00383396; gnomAD v4.1 reports highest South Asian AF 0.004325392468986717 and grpmax FAF 0.00397315.
• The variant is present in both datasets, so absence-based reasoning is not relevant; neither observed frequency approaches the stand-alone benign threshold.

Sources

Reasoning

No governing BAP1 VCEP or gene-specific framework was available, so the supplied generic BS1 threshold of >=0.01 was used. The highest observed population frequency is 0.004442121766396656 in gnomAD v2.1 South Asians, with gnomAD v4.1 at 0.004325392468986717; both are below 0.01. The corresponding grpmax FAF values, 0.00383396 and 0.00397315, are likewise below the threshold.

Rule

Generic ACMG BS1: allele frequency >=0.01; no applicable BAP1-specific specification was available.

Evidence considered

• No applicable BAP1 VCEP or gene-specific framework was available; the supplied generic ACMG BS1 threshold of >=0.01 was applied.
• gnomAD v2.1 reports highest South Asian AF 0.004442121766396656 and grpmax FAF 0.00383396; gnomAD v4.1 reports highest South Asian AF 0.004325392468986717 and grpmax FAF 0.00397315.
• The supplied non-cancer subsets were not governing-specification requirements here, because no applicable specification was found; the default all-comers gnomAD v2.1 and v4.1 entries were therefore used.

Sources

Reasoning

BP1 applies when missense variants are a common benign mechanism in a gene for which truncating variants are the primary disease mechanism. BAP1 is not shown here to have a primarily truncating disease mechanism: the reviewed literature reports truncating variants as 36% of BAP1 tumor mutations and documents functional effects for multiple missense variants. Thus the available gene-level evidence does not support BP1.

Rule

BP1: missense variant in a gene for which primarily truncating variants are known to cause disease.

Evidence considered

• The review reports that truncating mutations represented 36% of BAP1 mutations in a cited tumor cohort, not a predominant majority.
• The review describes in-vitro functional effects for BAP1 missense variants Phe81Val, Cys91Trp, and Ala95Asp, supporting that missense variation can be functionally relevant rather than presumptively benign.

Sources

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. ClinVar exactly matches NM_004656.4:c.121G>A (p.Gly41Ser), but the record has zero expert-panel submissions; its Benign and Likely benign classifications are from ordinary laboratory submissions. Those submissions cannot trigger BP6, so BP6 is not met.

Rule

BP6: apply only when an exact-variant ClinVar expert panel classifies the variant as Benign or Likely benign; ordinary submissions and aggregate labels do not qualify.

Evidence considered

• ClinVar exact-match record NM_004656.4(BAP1):c.121G>A (p.Gly41Ser) reports zero expert-panel submissions and ordinary laboratory classifications of Benign or Likely benign; these do not qualify for BP6 under the stated rule.

Still missing

• No exact-variant ClinVar expert-panel Benign or Likely benign classification.

Sources

Reasoning

PS2 requires a confirmed de novo variant in the proband with maternity and paternity confirmed, or equivalent parental testing. The available exact-variant reports describe the proband/individual and family history but provide no parental genotypes, parentage confirmation, or de novo determination for NM_004656.4:c.121G>A (p.Gly41Ser). Therefore PS2 cannot be assessed.

Rule

Generic ACMG/AMP PS2: confirmed de novo occurrence in the proband with maternity and paternity confirmed; insufficient parental evidence prevents assessment.

Evidence considered

• PMID:22683710 reports the exact germline c.121G>A (p.Gly41Ser) variant in one individual but does not report parental testing or a formal de novo assessment.
• PMID:23709298 identifies the exact variant in individual II:1 and discusses family cosegregation, but does not document parental genotypes or confirmed de novo origin.

Still missing

• Parental genotypes and maternity/paternity confirmation are not documented.
• The variant's de novo status in the reported individual is not established.

Sources

Reasoning

No applicable BAP1-specific VCEP or CSPEC specification was identified, so generic ACMG/AMP functional-evidence principles apply. The available publications report observation of NM_004656.4:c.121G>A (p.Gly41Ser) and family cosegregation information, but do not provide a validated cell-, protein-, or other disease-relevant functional assay for this exact variant, with assay controls and a quantitative result demonstrating abnormal function. The reported cosegregation study instead suggested that the variant was not responsible for the family's cancer predisposition, which is not PS3 functional evidence. Therefore PS3 cannot be assessed from the available evidence and no PS3 strength is assigned.

Rule

Generic ACMG/AMP PS3 requires well-established functional studies showing a damaging effect; no applicable BAP1-specific specification was available.

Evidence considered

• PMID:22683710 reports the exact germline c.121G>A (p.Gly41Ser) variant in an individual with a family history of renal cell carcinoma but reports no functional assay.
• PMID:23709298 reports the exact variant and states that cosegregation suggested it was not responsible for the family's cancer predisposition; it reports no functional assay.
• PMID:26166446 identifies the exact Gly41Ser variant in a germline-mutation summary and labels it probably benign, but provides no variant-specific functional assay result.
• PMID:24728327 does not report the exact BAP1 variant or BAP1-specific functional findings.
• PMID:26554828 reports cohort-level BAP1 mutation and expression data without reporting the exact c.121G>A variant or a variant-specific functional assay.

Still missing

• A validated disease-relevant functional assay for p.Gly41Ser with appropriate positive, negative, and wild-type controls and quantitative results is unavailable.

Sources

Reasoning

No governing VCEP specification or domain_tables entry is available for BAP1. A review describes the BAP1 catalytic domain as being in the N-terminal region, but does not provide a sufficiently precise validated boundary to establish that residue 41 lies within an approved critical functional domain for PM1. The same review also classifies Gly41Ser as probably benign, so the available evidence does not support applying PM1 automatically.

Rule

PM1: variant located in a mutational hot spot and/or critical functional domain without benign variation; apply only when the critical-domain boundaries are adequately established.

Evidence considered

• The BAP1 review states that the N-terminal region is where the catalytic domain should be, but it does not define exact amino-acid boundaries for that domain.
• The review's germline mutation table lists G121A (Gly41Ser) as probably benign.

Still missing

• A validated BAP1 critical-domain definition with residue boundaries is needed to determine whether Gly41 qualifies for PM1.

Sources

Reasoning

PM6 concerns a presumed de novo occurrence when maternity and/or paternity has not been confirmed. The exact-variant literature identifies an affected individual and family context but does not state that the variant was presumed de novo, does not provide parental testing, and does not establish an unconfirmed-parentage de novo event. Therefore PM6 cannot be assessed.

Rule

Generic ACMG/AMP PM6: presumed de novo occurrence without confirmation of maternity and/or paternity; a presumed de novo event is not documented here.

Evidence considered

• PMID:22683710 reports one individual with the exact germline variant and does not describe parental testing or presumed de novo status.
• PMID:23709298 reports the exact variant in individual II:1 and family cosegregation analysis, without a presumed de novo designation.

Still missing

• No report explicitly characterizes the variant as presumed de novo.
• Parental genotypes and parentage information are unavailable.

Sources

Reasoning

PP2 requires evidence that missense variation is a low-rate mechanism for benign variation in the gene and that missense variants are a recognized disease mechanism. The case materials establish BAP1 loss-of-function biology and document functional effects for some other missense variants, but provide no validated gene-level benign-missense depletion metric or framework threshold for applying PP2. Therefore PP2 is not assessed.

Rule

PP2: missense variants are a common mechanism of disease in the gene, and the gene has a low rate of benign missense variation.

Evidence considered

• The review describes functional assays for several BAP1 missense mutants, but those data do not establish the gene-level low benign-missense rate required for PP2.
• No BAP1-specific PP2 threshold or missense constraint metric is available in the governing framework or case evidence.

Still missing

• A validated BAP1 missense constraint or benign-missense rate supporting PP2 is needed.

Sources

Reasoning

Generic ACMG/AMP PP4 requires a patient's phenotype or family history to be highly specific for a disease with a single-gene etiology. The available evidence identifies a renal cell carcinoma family history in the published exact-variant report, but does not provide the current patient's clinical phenotype, diagnostic findings, or a sufficiently specific phenotype assessment. PP4 therefore cannot be assessed from the available evidence.

Rule

Generic ACMG/AMP PP4: patient's phenotype or family history is highly specific for a disease with a single-gene etiology; sufficient patient-level phenotype data are unavailable.

Evidence considered

• PMID:23709298 reports a family history of renal cell carcinoma around the exact-variant observation, but this does not establish the current patient's highly specific phenotype.

Still missing

• Patient-level phenotype and diagnostic findings are not available.
• No documented phenotype-specificity assessment linking the patient to a BAP1-associated disorder.

Sources

Reasoning

The population records report one homozygote in gnomAD v2.1 and six homozygotes in gnomAD v4.1, including six among South Asian individuals. However, the available records do not establish that these individuals were healthy, unaffected by BAP1 tumor-predisposition manifestations, age-appropriate for penetrance assessment, or clinically phenotyped. Because BAP1 tumor predisposition is an adult-onset cancer syndrome with potentially incomplete or age-dependent penetrance, unphenotyped gnomAD homozygotes alone do not satisfy the generic BS2 requirement for observation in healthy adults.

Rule

Generic ACMG BS2: observation of the variant in healthy adults, including homozygotes where relevant; unphenotyped population homozygote counts alone are insufficient when health status and age-dependent penetrance cannot be verified.

Evidence considered

• gnomAD v2.1 reports total homozygotes = 1, including one South Asian homozygote.
• gnomAD v4.1 reports total homozygotes = 6, all six in the South Asian population record.
• The available population records provide allele counts and homozygote counts but no individual-level phenotype, age, follow-up, or disease-ascertainment information; therefore the generic BS2 healthy-adult condition cannot be verified.

Still missing

• Individual-level health status and phenotype data for the reported homozygotes are unavailable.
• Age and follow-up information needed to address adult-onset and incomplete penetrance are unavailable.
• The records do not establish whether any homozygotes had BAP1 tumor-predisposition manifestations or ascertainment-related disease.

Sources

Reasoning

No applicable BAP1-specific VCEP or CSPEC specification was identified, so generic ACMG/AMP functional-evidence principles apply. The available publications do not report a validated functional assay for NM_004656.4:c.121G>A (p.Gly41Ser) demonstrating normal BAP1 function using appropriate controls and a quantitative, biologically relevant endpoint. Clinical observation, a probably benign tabular label, cohort-level BAP1 data, and cosegregation findings cannot substitute for direct normal functional evidence, and no BS3 strength is assigned.

Rule

Generic ACMG/AMP BS3 requires well-established functional studies showing no damaging effect; no applicable BAP1-specific specification was available.

Evidence considered

• PMID:22683710 reports the exact variant but no assay demonstrating normal BAP1 function.
• PMID:23709298 reports the exact variant and family cosegregation analysis but no functional assay or normal-function result.
• PMID:26166446 lists the exact Gly41Ser variant as probably benign in a review table, but this is not direct functional evidence and no assay result is reported.
• PMID:24728327 does not report the exact BAP1 variant or BAP1-specific functional findings.
• PMID:26554828 reports cohort-level BAP1 mutation and expression data without an exact-variant normal-function assay.

Still missing

• A validated disease-relevant assay demonstrating normal BAP1 function for p.Gly41Ser with appropriate controls and quantitative results is unavailable.

Sources

Reasoning

No applicable BAP1-specific framework was available, so generic ACMG/AMP is used. BP2 requires the evaluated variant to be observed in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant for a recessive disorder. The exact-variant literature reports c.121G>A (p.Gly41Ser) in a familial renal-cell-carcinoma evaluation and states that cosegregation suggested it was not responsible for the cancer predisposition, but it does not identify a pathogenic variant in trans or cis and does not establish the required phase. BP2 therefore cannot be assessed from the available evidence.

Evidence considered

• PMID:23709298 reports c.121G>A (p.G41S) in individual II:1 and states that cosegregation studies suggested the variant was not responsible for the family's cancer predisposition, but it does not report a pathogenic partner variant or cis/trans phase.
• PMID:26166446 repeats the same germline BAP1 Gly41Ser observation in an individual with familial renal-cell-carcinoma history, without reporting a pathogenic partner variant or phase information.
• The available evidence does not establish the specific co-occurrence and phase required by generic BP2.

Still missing

• A matched pathogenic variant and validated cis/trans phase are not reported for the individual carrying BAP1 c.121G>A (p.Gly41Ser).

Sources

Reasoning

Generic ACMG/AMP BP5 requires the variant to be found in an affected individual who also has an alternative molecular basis explaining the phenotype. The exact-variant literature reports that the individual had previously tested negative for a germline VHL mutation; this is not an alternative pathogenic molecular explanation. No current patient-level molecular finding or phenotype-linked alternative cause is documented, so BP5 cannot be assessed.

Rule

Generic ACMG/AMP BP5: variant found in an affected individual with an alternative molecular basis for the phenotype; the required alternative pathogenic explanation is not documented.

Evidence considered

• PMID:23709298 states that the exact-variant carrier had previously tested negative for a VHL mutation; a negative test is not an alternative molecular basis for the phenotype.
• PMID:22683710 likewise reports prior evaluation without an identified germline VHL mutation and does not provide an alternative pathogenic molecular diagnosis.

Still missing

• No documented affected-patient phenotype for the current case.
• No alternative pathogenic variant or molecular diagnosis explaining the phenotype.

Sources