NM_000465.4:c.221G>T

BARD1 · NP_000456.2:p.(Cys74Phe) · NM_000465.4

GRCh37: chr2:215657164 C>A · GRCh38: chr2:214792440 C>A

Gene: BARD1 Transcript: NM_000465.4

Final call

VUS

PM1 moderate PM2 moderate PP3 supporting

Variant details

Gene

BARD1

Transcript

NM_000465.4

Protein

NP_000456.2:p.(Cys74Phe)

gnomAD AF

9.186760720949761e-05 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

This variant resides in the BARD1 RING finger domain (p.Cys74Phe), a critical functional domain required for BRCA1 heterodimerization and E3 ubiquitin ligase activity.

The variant is extremely rare in population databases: absent from gnomAD v2.1 and observed at 0.0092% (135/1,469,506 alleles, 0 homozygotes) in gnomAD v4.1, meeting PM2 threshold (<0.1%).

Multiple in silico predictors support a deleterious effect: REVEL score 0.932 (strongly damaging), BayesDel score 0.560 (moderately deleterious). No splicing impact is predicted (SpliceAI max delta 0.05).

No functional studies have been reported for this variant. OncoKB reports unknown oncogenic effect. Six clinical laboratories in ClinVar classify this variant as Uncertain significance with 1-star review status.

No de novo observations, segregation data, case-control enrichment, or same-residue pathogenic comparators were identified. No literature publication mentions this specific variant.

Applying generic ACMG/AMP 2015 criteria: PM1 (RING domain) + PM2 (rare in population) + PP3 (in silico damaging) = 2 moderate + 1 supporting pathogenic criteria, with zero benign criteria met. This combination is insufficient for Likely Pathogenic classification and supports a classification of Uncertain significance.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	PVS1 is not applicable to missense variants. NM_000465.4:c.221G>T is a missense substitution (p.Cys74Phe) and does not fall into any null-variant category (nonsense, frameshift, or canonical ±1,2 splice consensus variants). The generic PVS1 framework per PMC6185798 does not apply to this variant class (variant_bucket: 'other', apply_generic_pvs1_framework: false).	pvs1_generic_framework pvs1_variant_assessment
PS1	Not met	PS1 requires the same amino acid change (p.Cys74Phe) from a different nucleotide change to be previously established as pathogenic. No evidence was identified of a different nucleotide substitution producing p.Cys74Phe with an established pathogenic classification.	clinvar
PS2	Not met	PS2 requires confirmed de novo occurrence. No de novo data were identified for NM_000465.4:c.221G>T in any available source.
PS3	Not met	PS3 requires well-established functional studies demonstrating a deleterious effect. No variant-specific or range-characterizing functional studies were identified for NM_000465.4:c.221G>T (p.Cys74Phe). The Color Health ClinVar submission (SCV000905903) explicitly noted that functional studies have not been reported for this variant. OncoKB reports Unknown Oncogenic Effect with no variant-specific reviewed functional evidence.	clinvar oncokb
PS4	Not met	PS4 requires a significantly increased prevalence of the variant in affected individuals compared to controls. No case-control data or statistical enrichment analysis was identified. The literature papers indexed under PS4 (24366376, 24366402, 24432435, 25394175, 26389258) are generic clinical practice guidelines and do not report variant-specific case observations.
PS5	Not met	PS5 (not a standard ACMG/AMP 2015 criterion) would require very strong evidence level functional or clinical data. No variant-specific data meeting this threshold were identified.
PM1	Met	The variant c.221G>T produces p.Cys74Phe, which resides in the BARD1 RING finger domain (residues ~46-90). The RING domain is critical for BARD1-BRCA1 heterodimerization and E3 ubiquitin ligase activity. C74 is a conserved cysteine within the zinc-coordinating RING structure. Missense alteration of a structurally critical RING domain residue meets PM1 at moderate strength per generic ACMG/AMP criteria.	clinvar gnomad_v4
PM2	Met	NM_000465.4:c.221G>T is absent from gnomAD v2.1 and present at very low frequency in gnomAD v4.1 (overall AF = 9.19e-05, 0.0092%; grpmax FAF = 8.91e-05). The allele frequency is well below the 0.1% threshold for PM2 application. Highest subpopulation frequency is in Ashkenazi Jewish (AF = 0.000112, 0.011%). No homozygotes observed.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	PM5 requires a different missense change at the same amino acid residue (p.Cys74) to be classified as pathogenic. Automated candidate harvesting found no same-residue pathogenic or likely pathogenic comparators for this position. Manual review of available evidence also did not identify any pathogenic comparator at residue 74.	pm5_candidates
PM6	Not met	PM6 requires a de novo observation without confirmation of paternity and maternity. No de novo data are available for this variant.
PP1	Not met	PP1 requires cosegregation of the variant with disease in multiple affected family members. No segregation data are available for this variant.
PP2	Not met	PP2 requires a low rate of benign missense variation in the gene and missense variants as a common disease mechanism. BARD1 is primarily a loss-of-function tumor suppressor; the gene's Z-score for missense constraint and rate of benign missense variation do not clearly meet PP2 criteria. Additionally, HCI prior data was not available for BARD1 in this analysis.
PP3	Met	Multiple in silico predictors support a deleterious effect for NM_000465.4:c.221G>T (p.Cys74Phe). REVEL score is 0.932, which is strongly predictive of pathogenicity (well above the 0.7 threshold). BayesDel score is 0.560, indicating moderate deleterious potential. SpliceAI predicts no significant splicing impact (max delta = 0.05), which does not contradict the missense assessment.	revel bayesdel spliceai
PP4	Not met	PP4 requires the patient's phenotype or family history to be highly specific for the disease associated with the gene. No patient-specific phenotype or family history data are available for assessment.
PP5	Not met	PP5 requires a reputable source to have reported the variant as pathogenic. In ClinVar, this variant (Variation ID: 234046) is classified as Uncertain significance by 6 clinical laboratories with review status 'criteria provided, single submitter' (1-star). No expert panel (3-star) classification exists. The ClinVar status does not meet the threshold for PP5 application. Literature indexed under PP5 (24366376, 24366402, 24432435, 25394175, 26389258) are generic clinical guideline documents that do not mention this specific variant.	clinvar
BA1	Not met	BA1 requires allele frequency >1% in population databases. The highest observed frequency is in gnomAD v4.1 Ashkenazi Jewish population (AF = 0.011%), well below the 1% threshold.	gnomad_v4
BS1	Not met	BS1 requires allele frequency >0.3% in population databases. The highest observed frequency is 0.011%, well below the 0.3% threshold.	gnomad_v4
BS2	Not met	BS2 requires observation in a healthy adult homozygous for a recessive disorder, or observation in trans with a pathogenic variant for a fully penetrant dominant disorder. No such data are available for this variant.
BS3	Not met	BS3 requires well-established functional studies demonstrating no deleterious effect. No functional studies (supporting or refuting) were identified for this variant.
BS4	Not met	BS4 requires lack of segregation with disease in affected family members. No segregation data are available for this variant.
BP1	Not met	BP1 applies to missense variants in genes where primarily truncating variants cause disease. While BARD1 is a tumor suppressor where loss-of-function is a recognized disease mechanism, missense variants within the RING domain (where p.Cys74Phe resides) have established pathogenic potential through disruption of BARD1-BRCA1 heterodimerization and E3 ubiquitin ligase activity. A RING domain missense is not appropriately downgraded by BP1, consistent with the evidence symmetry principle applied to PM1.
BP2	Not met	BP2 requires observation in trans with a pathogenic variant for a fully penetrant dominant disorder. No such observations are available.
BP4	Not met	BP4 requires multiple lines of computational evidence suggesting no impact on gene product. REVEL score is 0.932, strongly predicting a deleterious effect, and BayesDel is 0.560 (moderately deleterious). These scores contradict BP4 application.	revel bayesdel
BP5	Not met	BP5 requires the variant to be found in a case with an alternate molecular basis for disease. No such data are available.
BP6	Not met	BP6 requires a reputable source to have reported the variant as benign. ClinVar classifies this variant as Uncertain significance (6 submitters, 1-star review). No reputable source reports it as benign or likely benign.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splicing impact. NM_000465.4:c.221G>T is a missense variant (p.Cys74Phe), not synonymous.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.