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BARD1
Final classification
VUS
BARD1 c.221G>T · p.Cys74Phe
BARD1

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

Gene
BARD1
Transcript
NM_000465.4
HGVS · transcript:coding
NM_000465.4:c.221G>T
Consequence
N/A
GRCh38
chr2:214792440 C>A
GRCh37
chr2:215657164 C>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate, PP3 supporting; combination = 2 moderate + 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate, PP3 supporting; combination = 2 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM1PM2PP3 VUS
BARD1 c.221G>T

This variant resides in the BARD1 RING finger domain (p.Cys74Phe), a critical functional domain required for BRCA1 heterodimerization and E3 ubiquitin ligase activity.1 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%).2 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).3 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.4 No de novo observations, segregation data, case-control enrichment, or same-residue pathogenic comparators were identified. No literature publication mentions this specific variant.5 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.6

PM1 + PM2 + PP3 VUS
3 revelbayesdelspliceai ↗
5 pm5_candidates
6 PMID:25741868 ↗generic_acmg_combination_rules
Gene diagram · NM_000465.4 · variants mapped to exon structure
BARD1 NM_000465.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 20 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM1 moderate Pathogenic
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.
p.Cys74Phe maps to the BARD1 RING finger domain (residues ~46-90)RING domain is critical for BARD1-BRCA1 heterodimerization and ubiquitin ligase functionC74 is a structurally conserved cysteine in the zinc-coordinating RING architecture
PM2 moderate Pathogenic
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.
Absent from gnomAD v2.1 (exomes)gnomAD v4.1: 135/1469
PP3 supporting Pathogenic
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: 0.932 (deleteriousabove 0.7 threshold)BayesDel: 0.560 (moderate deleterious prediction)
Assessed · not applied
Pathogenic
PS1 PS1 requires the same amino acid change (p.Cys74Phe) from a different nucleotide change to be previously established as pathogenic.
PS2 PS2 requires confirmed de novo occurrence.
PS3 PS3 requires well-established functional studies demonstrating a deleterious effect.
PS4 PS4 requires a significantly increased prevalence of the variant in affected individuals compared to controls.
PM5 PM5 requires a different missense change at the same amino acid residue (p.Cys74) to be classified as pathogenic.
PM6 PM6 requires a de novo observation without confirmation of paternity and maternity.
PP1 PP1 requires cosegregation of the variant with disease in multiple affected family members.
PP2 PP2 requires a low rate of benign missense variation in the gene and missense variants as a common disease mechanism.
PP4 PP4 requires the patient's phenotype or family history to be highly specific for the disease associated with the gene.
PP5 PP5 requires a reputable source to have reported the variant as pathogenic.
Benign
BA1 BA1 requires allele frequency >1% in population databases.
BS1 BS1 requires allele frequency >0.3% in population databases.
BS2 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.
BS3 BS3 requires well-established functional studies demonstrating no deleterious effect.
BS4 BS4 requires lack of segregation with disease in affected family members.
BP1 BP1 applies to missense variants in genes where primarily truncating variants cause disease.
BP2 BP2 requires observation in trans with a pathogenic variant for a fully penetrant dominant disorder.
BP4 BP4 requires multiple lines of computational evidence suggesting no impact on gene product.
BP5 BP5 requires the variant to be found in a case with an alternate molecular basis for disease.
BP6 BP6 requires a reputable source to have reported the variant as benign.
N/A · 2 PVS1 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 9.18676e-05; MAF= 0.00919%, 135/1469506 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.000112284; MAF= 0.01123%, 3/26718 alleles, homozygotes = 0); grpmax FAF= 8.91e-05.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0092% · 135 / 1,469,506
0 hom · FAF 0.0089%
Ashkenazi Jewish
3 / 26,718
0.011%
European (Finnish)
6 / 56,436
0.011%
European (non-Finnish)
114 / 1,082,550
0.011%
African/African American
5 / 66,582
0.0075%
Remaining individuals
4 / 56,148
0.0071%
South Asian
3 / 82,260
0.0036%
+ 4 not observed (Admixed American, Amish, East Asian, Middle Eastern)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (6 clinical laboratories). (ClinVarID = 234046)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05). REVEL score = 0.932. BayesDel score = 0.560394.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BARD1, a tumor suppressor involved in the DNA damage response, is altered by mutation in breast and ovarian cancers.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV107297670, n = 3 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 7 PMIDs not cited in assessment
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
24366376 ↗ Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement. CLINVAR
24366402 ↗ Summaries for patients. Assessing the genetic risk for BRCA-related breast or ovarian cancer in women: recommendations from the U.S. Preventive Services Task Force. CLINVAR
24432435 ↗ PMID 24432435 CLINVAR
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR