ARID1A c.673C>T, p.(Pro225Ser)

Reasoning

No applicable ARID1A-specific VCEP or gene framework was identified, so the generic ACMG/AMP rule applies. PM2 supports rarity or absence in population databases. The variant is absent from gnomAD v2.1 and from the reported gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer subset queries; in the larger gnomAD v4.1 dataset it remains extremely rare at 4/1,496,722 total alleles (AF 2.67251e-06), with zero homozygotes and grpmax FAF 3.804e-05. This supports PM2 at supporting strength.

Rule

Generic ACMG/AMP PM2: absent or extremely rare in population databases; applied here at supporting strength because the variant is not fully absent from the largest available dataset.

Evidence considered

• No official CSPEC/VCEP or local ARID1A-specific population framework was available; generic ACMG/AMP criteria were used.
• gnomAD v2.1 exomes: variant absent.
• The case data report absence from gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer subset queries.
• gnomAD v4.1: 4/1,496,722 total alleles, AF 2.67251e-06, zero homozygotes, and grpmax FAF 3.804e-05.

Sources

Reasoning

PP2 is not met because the available ARID1A evidence supports a loss-of-function tumor-suppressor mechanism but does not establish that missense variation is a common disease mechanism with little benign missense variation. The variant is absent from ClinVar and has only rare population observation in gnomAD v4.1 (AF 2.67251e-06; 4/1,496,722 alleles), which does not establish the PP2 gene-level requirement.

Rule

PP2 requires a missense mechanism that is common for the gene and little benign missense variation in a gene where missense variation is a known disease mechanism.

Evidence considered

• gnomAD v4.1 reports 4/1,496,722 alleles and total AF 2.67251e-06.
• ClinVar has no record for the variant.
• The available gene context describes ARID1A primarily as a loss-of-function tumor suppressor and does not establish a missense-driven disease mechanism.

Still missing

• A validated gene-level demonstration that ARID1A disease is commonly caused by missense variants with little benign missense variation is needed.

Sources

Reasoning

No ARID1A ClinGen CSPEC or other gene-specific VCEP framework was retrieved. Under the requested group rule, PP5 may be applied only when the exact variant has a ClinVar expert-panel classification of Pathogenic or Likely pathogenic. The case evidence states that NM_006015.5:c.673C>T is absent from ClinVar; consequently, there is no exact-variant expert-panel Pathogenic/Likely pathogenic assertion. No ordinary laboratory submission, aggregate ClinVar label, or non-expert assertion is available or eligible to trigger PP5.

Rule

PP5 is met only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification; none is present.

Evidence considered

• The ClinVar evidence reports that NM_006015.5:c.673C>T is absent from ClinVar, with no exact-variant classification or expert-panel assertion.
• Per the requested rule, PP5 requires an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification; ordinary laboratory submissions, aggregate labels, and non-expert assertions cannot trigger PP5.

Sources

Reasoning

No applicable ARID1A-specific VCEP or gene framework was identified, so the generic ACMG/AMP rule applies. BA1 requires a population allele frequency above 5%. The variant is absent from gnomAD v2.1 and is present at only 4/1,496,722 total alleles in gnomAD v4.1 (AF 2.67251e-06); the highest reported population AF is 4/35,782 (1.11788e-04), far below the BA1 threshold. Therefore BA1 is not met.

Rule

Generic ACMG/AMP BA1: allele frequency >5% in population databases.

Evidence considered

• No official CSPEC/VCEP or local ARID1A-specific population framework was available; generic ACMG/AMP criteria were used.
• gnomAD v2.1 exomes: variant absent.
• gnomAD v4.1: 4/1,496,722 total alleles, total AF 2.67251e-06, zero homozygotes; highest reported subgroup AF 4/35,782 = 1.11788e-04.
• The case data also report absence from gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer subsets.

Sources

Reasoning

No applicable ARID1A-specific VCEP or gene framework was identified, so the generic ACMG/AMP rule applies. BS1 requires an allele frequency greater than expected for the disorder, which must be interpreted against disease prevalence, inheritance, penetrance, and allelic contribution. The variant is absent from gnomAD v2.1 and has a gnomAD v4.1 total AF of 2.67251e-06, grpmax FAF of 3.804e-05, and highest reported subgroup AF of 1.11788e-04. These frequencies do not provide positive evidence that the variant is too common for a rare dominant ARID1A disorder, so BS1 is not met.

Rule

Generic ACMG/AMP BS1: allele frequency greater than expected for the disorder, accounting for prevalence, penetrance, inheritance, and allelic contribution.

Evidence considered

• No official CSPEC/VCEP or local ARID1A-specific population framework was available; generic ACMG/AMP criteria were used.
• gnomAD v2.1 exomes: variant absent.
• gnomAD v4.1: total AF 2.67251e-06, grpmax FAF 3.804e-05, and highest reported subgroup AF 1.11788e-04 (4/35,782).
• No disease-specific prevalence, penetrance, or maximum credible allele-frequency threshold was supplied for ARID1A; the observed frequency is nevertheless far below common benign-frequency ranges.

Sources

Reasoning

No applicable ARID1A-specific VCEP or gene framework was identified, so the generic ACMG/AMP rule applies. BS2 requires observation of the variant in healthy adults at an age when the associated disorder would be expected to manifest, including appropriate homozygote or hemizygote observations where relevant. gnomAD v4.1 reports zero homozygotes and only 4 total alleles, while gnomAD v2.1 reports the variant as absent; the available population data therefore do not demonstrate the required healthy-adult observation pattern. BS2 is not met.

Rule

Generic ACMG/AMP BS2: observed in a healthy adult individual at an age when disease would be expected to manifest, including relevant homozygote or hemizygote observations.

Evidence considered

• No official CSPEC/VCEP or local ARID1A-specific population framework was available; generic ACMG/AMP criteria were used.
• gnomAD v4.1: 4/1,496,722 total alleles and zero homozygotes; all reported subgroup homozygote counts are zero.
• gnomAD v2.1 exomes: variant absent.
• The available population records do not establish that unaffected adults carrying the variant were observed at an age when ARID1A-associated disease would be expected to manifest.

Sources

Reasoning

No ARID1A ClinGen CSPEC or other gene-specific VCEP framework was retrieved. Under the requested group rule, BP6 may be applied only when the exact variant has a ClinVar expert-panel classification of Benign or Likely benign. The case evidence states that NM_006015.5:c.673C>T is absent from ClinVar; therefore, no exact-variant expert-panel Benign/Likely benign assertion exists. Ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions cannot trigger BP6.

Rule

BP6 is met only for an exact-variant ClinVar expert-panel Benign or Likely benign classification; none is present.

Evidence considered

• The ClinVar evidence reports that NM_006015.5:c.673C>T is absent from ClinVar, with no exact-variant classification or expert-panel assertion.
• Per the requested rule, BP6 requires an exact-variant ClinVar expert-panel Benign or Likely benign classification; ordinary laboratory submissions, aggregate labels, and non-expert assertions cannot trigger BP6.

Sources

Reasoning

PS1 cannot be assessed because the case contains no ClinVar record, literature PMID, or other validated evidence documenting a pathogenic or likely pathogenic variant producing the same amino-acid change p.Pro225Ser.

Rule

PS1 requires a different nucleotide change producing the same amino-acid change and established pathogenic or likely pathogenic evidence for that comparator.

Evidence considered

• ClinVar returned no record for NM_006015.5:c.673C>T, and the literature packet contained zero PMIDs; therefore same-amino-acid PS1 evidence is unavailable.

Still missing

• A validated pathogenic or likely pathogenic same-amino-acid comparator is needed.

Sources

Reasoning

No case-level information documents a confirmed de novo occurrence of NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser), including proband phenotype, parental genotypes, maternity/paternity confirmation, or the number and quality of independent de novo observations. The available evidence bundle contains no applicable ARID1A-specific VCEP specification, so generic ACMG/AMP de novo criteria would require these missing data before PS2 can be assessed.

Rule

Generic ACMG/AMP PS2: confirmed de novo occurrence in a patient with a phenotype consistent with the disease, with maternity and paternity confirmed; strength depends on the number and quality of observations.

Evidence considered

• The case materials identify the variant as NM_006015.5:c.673C>T, predicted to encode NP_006006.3:p.Pro225Ser, but provide no family-study or de novo testing results.
• No applicable ARID1A-specific VCEP framework is available; generic ACMG/AMP assessment is therefore the applicable fallback, but its PS2 data requirements are not met by the available case information.

Still missing

• Documented proband phenotype consistent with an ARID1A-related disorder
• Parental testing results showing both parents lack the variant
• Confirmation of maternity and paternity
• Number of independent de novo observations and test-quality details

Reasoning

No variant-specific validated functional assay was identified for ARID1A NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser). The available evidence contains no experimental measurements, assay controls, biologically relevant system, or quantitative result demonstrating an adverse effect. OncoKB specifically reports no variant-specific reviewed functional evidence. Therefore, PS3 cannot be assigned at any strength.

Evidence considered

• The consolidated evidence reports no variant-specific validated functional assay or experimental result for NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser).
• OncoKB states that it did not identify variant-specific reviewed functional evidence for this variant; its available information is gene-level context rather than an assay result.

Still missing

• A validated assay measuring the relevant ARID1A biological function for p.Pro225Ser is needed.
• Assay controls, experimental context, and quantitative comparison with wild-type and known damaging controls are unavailable.

Sources

Reasoning

No ARID1A ClinGen CSPEC or other gene-specific VCEP framework was retrieved, so generic ACMG/AMP guidance is used. PS4 requires a statistically significant excess of the variant in affected individuals compared with appropriate controls. The case evidence contains no affected-case/control counts, odds ratio, relative risk, hazard ratio, p-value, confidence interval, or exact-variant case-control study for NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser). The variant is absent from ClinVar and no literature PMIDs were identified, so PS4 cannot be evaluated from the available evidence.

Rule

Generic ACMG/AMP PS4: the prevalence of the variant in affected individuals is significantly increased compared with controls; case-control evidence is required.

Evidence considered

• Generic ACMG/AMP PS4 requires statistically significant increased prevalence of the variant in affected individuals compared with controls; no gene-specific VCEP rule was available.
• The case evidence contains no exact-variant case-control dataset, affected/control counts, odds ratio, relative risk, hazard ratio, p-value, or confidence interval for NM_006015.5:c.673C>T (ARID1A p.Pro225Ser).

Still missing

• An exact-variant case-control study or validated affected-versus-control enrichment analysis with counts and statistical uncertainty is required.

Reasoning

PM1 cannot be assessed because no applicable ARID1A VCEP framework or authoritative domain table was retrieved, and the available case evidence does not establish that residue 225 lies in a well-established critical functional domain or mutational hotspot. The hotspot search was negative, but the absence of residue-level domain boundaries prevents a complete PM1 domain assessment.

Rule

PM1 requires a variant located in a well-established critical functional domain or mutational hotspot without benign variation sufficient to undermine the observation.

Evidence considered

• The case reports no statistically significant ARID1A P225 hotspot.
• No ARID1A VCEP framework or domain_tables entry was available; general gene descriptions do not provide residue-level domain boundaries.

Still missing

• An applicable ARID1A framework or authoritative residue-level functional-domain map is needed.

Reasoning

No applicable ARID1A-specific VCEP or gene-specific framework was available, so generic ACMG/AMP 2015 guidance was used. PM3 requires observation of the tested variant in trans with a pathogenic or likely pathogenic variant in an affected individual, generally supporting a recessive disease mechanism. The available evidence contains no affected-proband observations, no second pathogenic or likely pathogenic variant, no phase information, and no documented inheritance mode for NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser). Therefore, PM3 cannot be adjudicated.

Rule

Generic ACMG/AMP 2015 PM3: apply only when the variant is observed in trans with a pathogenic or likely pathogenic variant in an affected individual with a recessive disorder; phase and disease context must be established.

Evidence considered

• No ARID1A-specific VCEP or gene-specific framework was available; the case identifies generic ACMG/AMP 2015 guidance as the fallback framework.
• The case evidence documents NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser), but provides no affected-proband observation, second pathogenic/likely pathogenic allele, phase result, or inheritance information needed for PM3.

Still missing

• Affected-proband data are absent.
• No pathogenic or likely pathogenic allele in the same proband is documented.
• No cis/trans phase information is available.
• The inheritance mode relevant to this case is not documented.

Sources

Reasoning

PM5 cannot be assessed because no same-residue comparator variants at ARID1A residue 225 were identified in the case evidence, and no validated pathogenic or likely pathogenic alternate missense change at that residue is available for comparison.

Rule

PM5 requires an established pathogenic missense variant at the same amino-acid residue but involving a different amino-acid substitution.

Evidence considered

• The PM5 candidate artifact reports zero same-residue candidates and instructs that PM5 not be applied from that artifact alone.

Still missing

• A validated pathogenic or likely pathogenic alternate missense comparator at residue 225 is needed.

Sources

Reasoning

No case-level information documents a presumed de novo occurrence of NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser) in an affected proband, and there are no parental genotypes, maternity/paternity data, or independent observations. Because no ARID1A-specific VCEP specification is available, the generic ACMG/AMP PM6 framework applies, but the evidence needed to distinguish a presumed from a confirmed de novo event is absent.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence in a patient with the phenotype, without confirmation of maternity and/or paternity; the presumption must be supported by case documentation.

Evidence considered

• The available case materials contain no report of the variant in an affected proband with parental testing or a documented presumed de novo basis.
• No applicable ARID1A-specific VCEP framework is available; generic ACMG/AMP PM6 assessment is the fallback, but its required case-level evidence is missing.

Still missing

• Affected proband phenotype and diagnostic context
• Parental genotypes or explicit unavailability of testing
• Maternity and paternity confirmation or documented basis for presumption
• Independent case count and laboratory validation details

Reasoning

No affected and unaffected relatives, pedigrees, variant-positive relatives, variant-negative relatives, or meioses are reported for NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser). Therefore, there is no segregation or phenotype-consistency dataset from which to assess PP1 at supporting, moderate, or strong strength under the generic ACMG/AMP framework.

Rule

Generic ACMG/AMP PP1: cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease; strength is calibrated to the number of informative meioses and the quality of segregation evidence.

Evidence considered

• No family segregation data or informative meioses are present in the available case materials.
• No applicable ARID1A-specific VCEP specification is available, so generic ACMG/AMP PP1 assessment would require documented cosegregation in affected relatives.

Still missing

• Pedigree and family structure
• Number of informative meioses
• Genotypes and phenotypes of affected relatives
• Genotypes and phenotypes of unaffected relatives
• Assessment of phenocopies and reduced penetrance

Reasoning

The variant is a missense substitution, NM_006015.5:c.673C>T (p.Pro225Ser), so PP3 is in scope through the calibrated missense-computational path. No REVEL score is available and no BayesDel score is available; therefore, there is no calibrated missense predictor evidence to support PP3. The SpliceAI max delta score is 0.001, but the SpliceAI path is reserved here for splice-region/intronic variants and is not used to assess this exonic missense variant.

Evidence considered

• NM_006015.5:c.673C>T is annotated as the missense variant p.Pro225Ser.
• No REVEL score was available for this variant.
• No BayesDel score was available for this variant.
• SpliceAI reported a maximum delta score of 0.001, but this exonic missense variant is not being evaluated through the splice-region/intronic SpliceAI path.

Still missing

• A calibrated REVEL score with an applicable published threshold is unavailable.
• A calibrated BayesDel score with a verified published threshold is unavailable.

Reasoning

No ARID1A ClinGen CSPEC or other gene-specific VCEP framework was retrieved, so generic ACMG/AMP guidance is used. PP4 requires a phenotype or highly specific disease presentation that is highly specific for the relevant disorder. This case provides no proband phenotype, clinical diagnosis, family history, or disease-specific presentation for NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser). Therefore phenotype specificity cannot be assessed and PP4 cannot be assigned.

Rule

Generic ACMG/AMP PP4: the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• Generic ACMG/AMP PP4 requires a phenotype or highly specific disease presentation for the relevant disorder; no gene-specific VCEP rule was available.
• No proband phenotype, clinical diagnosis, family history, or disease-specific presentation is included in the available case evidence.

Still missing

• A documented proband phenotype and relevant clinical diagnosis or family-history details are required to assess phenotype specificity.

Reasoning

No variant-specific validated functional assay was identified for ARID1A NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser). The available evidence contains no experimental measurements, assay controls, biologically relevant system, or quantitative result demonstrating preserved normal function. OncoKB specifically reports no variant-specific reviewed functional evidence. Therefore, BS3 cannot be assigned at any strength.

Evidence considered

• The consolidated evidence reports no variant-specific validated functional assay or experimental result for NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser).
• OncoKB states that it did not identify variant-specific reviewed functional evidence for this variant; its available information is gene-level context rather than an assay result.

Still missing

• A validated assay measuring the relevant ARID1A biological function for p.Pro225Ser is needed.
• Assay controls, experimental context, and quantitative comparison with wild-type and known benign controls are unavailable.

Sources

Reasoning

No family pedigree, unaffected relatives, genotype results, phenotype assessments, or penetrance information is provided for NM_006015.5:c.673C>T (NP_006006.3:p.Pro225Ser). Consequently, absence of segregation in clinically relevant relatives cannot be evaluated, and BS4 cannot be assigned as evidence against pathogenicity.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family; assessment requires an informative pedigree and consideration of penetrance, age, phenocopies, and phenotype reliability.

Evidence considered

• The available case materials contain no non-segregation observations or family data for this variant.
• No applicable ARID1A-specific VCEP framework is available; generic ACMG/AMP BS4 assessment requires affected-status and genotype data from relevant unaffected relatives.

Still missing

• Pedigree and relevant relatives
• Reliable clinical phenotyping of relatives
• Genotypes of unaffected relatives
• Penetrance, age-related expression, and phenocopy considerations

Reasoning

BP1 cannot be assessed conclusively because the available evidence supports ARID1A loss of function as a disease mechanism but does not document that pathogenic ARID1A disease is predominantly caused by truncating variants such that missense variants are usually benign. The variant's very low gnomAD v4.1 frequency (AF 2.67251e-06) is not sufficient to establish BP1.

Rule

BP1 requires a missense variant in a gene for which pathogenic disease is established to be caused primarily by truncating variants.

Evidence considered

• The available gene context supports ARID1A loss of function but does not quantify the pathogenic variant spectrum or establish predominant truncating inheritance.
• gnomAD v4.1 reports total AF 2.67251e-06 for this variant, which is not a gene-level BP1 demonstration.

Still missing

• A gene-level spectrum showing predominant truncating pathogenic variation and generally benign missense variation is needed.

Sources

Reasoning

No applicable ARID1A-specific VCEP or gene-specific framework was available, so generic ACMG/AMP 2015 guidance was used. BP2 requires a reliable observation of the variant in trans with a pathogenic variant for a dominant disorder, or in cis with a pathogenic variant for a recessive disorder, with the relevant disease and phase context established. The available evidence contains no affected-proband or family observations, no additional pathogenic or likely pathogenic allele, no cis/trans phase information, and no documented inheritance mode. Therefore, BP2 cannot be adjudicated.

Rule

Generic ACMG/AMP 2015 BP2: apply only when the variant is observed in trans with a pathogenic variant for a dominant disorder or in cis with a pathogenic variant for a recessive disorder, with phase and disease context established.

Evidence considered

• No ARID1A-specific VCEP or gene-specific framework was available; the case identifies generic ACMG/AMP 2015 guidance as the fallback framework.
• The case evidence provides no paired pathogenic/likely pathogenic allele, no phase determination, no affected-proband or family context, and no inheritance mode for evaluating BP2.

Still missing

• No observation of the tested variant with another pathogenic or likely pathogenic allele is documented.
• No cis/trans phase information is available.
• No affected-proband or family segregation context is available.
• The inheritance mode relevant to this case is not documented.

Sources

Reasoning

The variant is a missense substitution, NM_006015.5:c.673C>T (p.Pro225Ser), so BP4 is in scope through the calibrated missense-computational path. No REVEL score is available and no BayesDel score is available; consequently, the available evidence cannot establish a calibrated benign computational prediction for BP4. The SpliceAI max delta score is 0.001, but the SpliceAI path is reserved here for splice-region/intronic variants and is not used to assess this exonic missense variant.

Evidence considered

• NM_006015.5:c.673C>T is annotated as the missense variant p.Pro225Ser.
• No REVEL score was available for this variant.
• No BayesDel score was available for this variant.
• SpliceAI reported a maximum delta score of 0.001, but this exonic missense variant is not being evaluated through the splice-region/intronic SpliceAI path.

Still missing

• A calibrated REVEL score with an applicable published threshold is unavailable.
• A calibrated BayesDel score with a verified published threshold is unavailable.

Reasoning

No ARID1A ClinGen CSPEC or other gene-specific VCEP framework was retrieved, so generic ACMG/AMP guidance is used. BP5 requires evidence that the affected phenotype is better explained by an alternative molecular basis, such as a different pathogenic variant or diagnosis. The case evidence contains no proband phenotype, alternate pathogenic variant, alternate molecular diagnosis, or validated likelihood-ratio-style BP5 result. Accordingly, BP5 cannot be evaluated. No numeric BP5 threshold is provided by the applicable generic framework, so no threshold comparison is possible.

Rule

Generic ACMG/AMP BP5: a different molecular basis explains the patient's phenotype; the available case evidence does not document one.

Evidence considered

• Generic ACMG/AMP BP5 concerns an alternate molecular basis for the patient's phenotype; no gene-specific VCEP rule was available.
• No alternate pathogenic variant, alternate molecular diagnosis, phenotype, or validated BP5 likelihood-ratio evidence is present in the case evidence.

Still missing

• A documented phenotype and confirmed alternative molecular basis of disease are required to assess BP5.