LYFE Sciences · Project HERA
Variant Interpretation · Classification Report
Generated: 2026-07-27
Case ID: NM_005732.3_c.221A_C_20260727_071438
Framework: ACMG/AMP 2015
Variant classification summary

NM_005732.3:c.221A>C

RAD50  · NP_005723.2:p.(Gln74Pro)  · NM_005732.3
GRCh37: chr5:131911476 A>C  ·  GRCh38: chr5:132575784 A>C
Gene: RAD50 Transcript: NM_005732.3
Final call
Likely Benign
PM2 moderate BP1 supporting benign BP4 supporting benign
All criteria require review: For research and educational purposes only.
Variant details
Gene
RAD50
Transcript
NM_005732.3
Protein
NP_005723.2:p.(Gln74Pro)
gnomAD AF
1.8812598922916003e-06 (v4.1)
ClinVar
Uncertain significance
OncoKB
Unknown Oncogenic Effect
Classification rationale
Interpretation summary
Generated evidence synthesis
1
NM_005732.3:c.221A>C (p.Gln74Pro) is a missense variant in RAD50, a gene in which biallelic loss-of-function variants cause RAD50 deficiency (OMIM #613078), an autosomal recessive disorder of DNA double-strand break repair.
2
This variant is absent from gnomAD v2.1 and observed at extremely low frequency in gnomAD v4.1 (3/1,594,676 total alleles, AF=1.88e-6, 0 homozygotes), with all three alleles restricted to the European (non-Finnish) subpopulation (grpmax FAF=6.9e-7). This extreme rarity meets PM2 at moderate strength.
3
REVEL (0.263), BayesDel (-0.354), and SpliceAI (max delta 0.01) all predict no damaging effect on protein function or splicing, meeting BP4 at supporting benign strength.
4
As a missense variant in a gene where truncating variants are the established disease mechanism, BP1 applies at supporting benign strength.
5
ClinVar reports this variant as Uncertain Significance (variation ID 1053169) based on two clinical laboratory submissions (Ambry Genetics and Invitae/Labcorp); no expert panel review is available. This does not meet criteria for PP5 or BP6, as neither pathogenic nor benign consensus has been reached.
6
No variant-specific functional studies, de novo observations, case-control data, segregation data, or published case reports were identified for this variant. OncoKB reports unknown oncogenic effect with no curated functional evidence.
7
Overall, the evidence profile consists of one moderate pathogenic criterion (PM2) and two supporting benign criteria (BP1, BP4). The net classification is Variant of Uncertain Significance (VUS) under the ACMG/AMP 2015 framework.
Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Benign classification because either one strong benign criterion plus one supporting benign criterion, or at least two supporting benign criteria, are present.
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: NM_005732.3:c.221A>C is a missense variant (p.Gln74Pro) in exon 3 of 25. It does not fall into any null-variant bucket (nonsense, frameshift, or canonical ±1,2 splice consensus) required for generic PVS1 framework assessment per ClinGen SVI recommendations (PMC6185798).
pvs1_generic_framework
PS1 Not met No alternate nucleotide change at c.221 resulting in the same amino acid change (p.Gln74Pro) has been established as pathogenic. PS1 requires a different nucleotide substitution at the same codon that produces the same missense change and is known to be pathogenic.
clinvar
PS2 Not met No de novo occurrence data available for this variant. PS2 requires confirmation of a de novo variant with both maternity and paternity confirmed.
PS3 Not met No variant-specific experimental functional data identified. OncoKB reports unknown oncogenic effect with no variant-level functional evidence. No publications with functional characterization of NM_005732.3:c.221A>C (p.Gln74Pro) were identified. The available in silico predictions (REVEL 0.263, BayesDel -0.354) suggest no damaging effect.
oncokb
PS4 Not met No case-control data demonstrating statistically significant enrichment of this variant in affected individuals. ClinVar records two clinical laboratory submissions (both VUS), but no case counts, odds ratios, or statistical comparison against controls is available.
clinvar
PS5 Not met No established pathogenic variant with the same amino acid change (p.Gln74Pro) has been reported independently. PS5 requires that the identical amino acid change, regardless of nucleotide change, be previously established as pathogenic.
clinvar
PM1 Not met This variant does not lie in a statistically significant hotspot per cancerhotspots.org, and there is insufficient evidence that residue 74 resides in a well-established critical functional domain without benign variation. While position 74 may be within the N-terminal ABC-ATPase domain of RAD50, no domain-level PM1 framework or CSPEC guidance is available to support application.
PM2 Met This variant is absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (3/1,594,676 alleles, AF=0.000000188, grpmax FAF=6.9e-7), well below the 0.1% PM2 threshold. All three alleles are in the European (non-Finnish) population with zero homozygotes.
gnomad_v2 gnomad_v4
PM5 Not met No pathogenic missense variant at amino acid position 74 with a different amino acid change was identified. The PM5 candidate pipeline found zero same-residue comparator variants with pathogenic classification in ClinVar.
pm5_candidates
PM6 Not met No de novo report available for this variant. PM6 requires a de novo observation with confirmed maternity and paternity, without confirmation that the variant occurred de novo.
PP1 Not met No co-segregation data available. PP1 requires demonstration that the variant co-segregates with disease in multiple affected family members.
PP2 Not met RAD50 disease (RAD50 deficiency, OMIM #613078) is primarily caused by biallelic loss-of-function variants. Missense variants are not the established common disease mechanism, and there is insufficient evidence that RAD50 has a low rate of benign missense variation (no gene-specific missense constraint z-score available).
pvs1_gene_context
PP3 Not met Multiple lines of computational evidence suggest no damaging effect. REVEL score is 0.263 (below 0.5 pathogenic threshold), BayesDel score is -0.354 (benign-leaning), and SpliceAI predicts no splice impact (max delta 0.01). These results do not support a deleterious effect and instead support benign interpretation (see BP4).
revel bayesdel spliceai
PP4 Not met No patient phenotype or family history data available for review. PP4 requires that the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.
PP5 Not met ClinVar reports this variant as Uncertain Significance (2 clinical laboratories), not pathogenic. No expert panel review available (1-star review status: criteria provided, single submitter). PP5 requires a reputable source to have classified the variant as pathogenic when independent evidence is not available for review.
clinvar
BA1 Not met The variant allele frequency in gnomAD v4.1 is 0.000019% (3/1,594,676 alleles), far below the 1% BA1 threshold.
gnomad_v4
BS1 Not met The variant allele frequency in gnomAD v4.1 is 0.000019% (3/1,594,676 alleles; grpmax FAF=6.9e-7), far below the 0.3% BS1 threshold for a non-VCEP assessment.
gnomad_v4
BS2 Not met While this variant is observed in gnomAD (3 alleles in presumably healthy population controls), no specific healthy adult individual with confirmed phenotype has been documented. BS2 requires an explicit observation of the variant in a healthy adult individual where full penetrance is expected at an early age. The mere presence in population databases, especially at extremely low frequency, does not satisfy BS2 without confirmatory phenotype data.
gnomad_v4
BS3 Not met No well-established in vitro or in vivo functional studies demonstrate that this variant has no damaging effect on protein function or splicing. OncoKB reports unknown oncogenic effect with no variant-specific functional characterization. In silico predictions (REVEL 0.263, BayesDel -0.354) are computational, not functional data.
oncokb revel bayesdel
BS4 Not met No segregation data available showing lack of co-segregation with disease in affected family members.
BP1 Met NM_005732.3:c.221A>C is a missense variant in RAD50, a gene for which the established germline disease mechanism is biallelic loss-of-function. RAD50 deficiency (OMIM #613078) is caused by truncating variants and other null alleles. A missense variant in a gene where truncating variants are the primary disease mechanism carries lower prior probability of pathogenicity.
pvs1_gene_context
BP2 Not met No data available regarding observation of this variant in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant.
BP4 Met Multiple lines of computational evidence support a benign interpretation. REVEL score is 0.263 (below the commonly applied 0.5 threshold for pathogenicity), BayesDel score is -0.354 (negative/benign-leaning), and SpliceAI predicts no splice-altering effect (max delta score 0.01).
revel bayesdel spliceai
BP5 Not met No observation of this variant in a case where an alternate molecular basis for disease has been identified.
BP6 Not met ClinVar reports this variant as Uncertain Significance (2 clinical laboratories), not benign or likely benign. BP6 requires a reputable source to have classified the variant as benign when independent evidence is not available for review.
clinvar
BP7 N/A Not applicable: NM_005732.3:c.221A>C is a missense (nonsynonymous) variant, not a synonymous variant. BP7 applies exclusively to silent/synonymous variants.
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