Variant classification summary

NM_005732.3:c.2033_2034dup

RAD50 · NP_005723.2:p.(Cys680HisfsTer41) · NM_005732.3

GRCh37: chr5:131931327 C>CAG · GRCh38: chr5:132595635 C>CAG

Gene: RAD50 Transcript: NM_005732.3

Final call

Likely Pathogenic

PVS1 strong PM2 supporting PP5 supporting

Variant details

Gene

RAD50

Transcript

NM_005732.3

Protein

NP_005723.2:p.(Cys680HisfsTer41)

gnomAD AF

2.4782256895353203e-06 (v4.1)

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_005732.3:c.2033_2034dup is a frameshift 2bp duplication in exon 13 of RAD50, predicted to cause premature termination at codon 720 (p.Cys680HisfsTer41). RAD50 loss of function is an established mechanism for NBS-like disorder.

2

This variant is extremely rare in population databases, absent from gnomAD v2.1 and gnomAD-Canada, with an allele frequency of 2.48e-6 (4/1,614,058 alleles, no homozygotes) in gnomAD v4.1, well below the PM2 threshold of 0.1%.

3

This variant has been classified as Pathogenic in ClinVar by two clinical laboratories (Ambry Genetics, Labcorp Genetics).

4

No variant-specific functional studies (PS3/BS3), de novo data (PS2/PM6), segregation data (PP1/BS4), or case-control enrichment data (PS4) were identified in the reviewed literature.

5

Applying generic ACMG/AMP 2015 combination rules: PVS1 (Strong) + PM2 (Supporting) + PP5 (Supporting) = 1 Strong + 2 Supporting, which meets the threshold for Likely Pathogenic classification.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Pathogenic classification based on the observed combination of pathogenic criteria.

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	Met	NM_005732.3:c.2033_2034dup is a 2bp duplication in exon 13 producing a frameshift and premature termination at codon 720 (p.Cys680HisfsTer41), well upstream of the native stop at codon 1313. NMD is expected. RAD50 loss of function is an established mechanism for NBS-like disorder (NBSLD), supported by germline disease literature. Under the ClinGen SVI PVS1 generic framework (PMC6185798), this frameshift null variant in a gene with confirmed LoF disease mechanism qualifies for PVS1 at strong strength.	pvs1_gene_context pvs1_variant_assessment pvs1_generic_framework
PS1	N/A	PS1 applies to variants resulting in the same amino acid change as an established pathogenic missense variant. This is a frameshift variant; PS1 is not applicable.
PS2	Not assessed	No de novo data are available for this variant.
PS3	Not assessed	No variant-specific functional studies were identified for NM_005732.3:c.2033_2034dup. The literature search returned RAD50 gene-level functional studies (mouse Rad50 models, yeast Mre11 complex studies) but none examined this specific variant.
PS4	Not met	Two clinical laboratories have classified this variant as Pathogenic in ClinVar, but no case-level enrichment data (case counts vs. controls) are available. The available submissions do not meet the PS4 threshold for case-control statistical significance.	clinvar
PS5	N/A	PS5 is not applicable to frameshift variants. This criterion applies to de novo observation of a recessive pathogenic missense variant in trans.
PM1	Not met	Variant c.2033_2034dup is in exon 13 encoding the coiled-coil domain of RAD50, but this specific residue/region is not a statistically significant mutational hotspot in the hotspot database. No ClinGen-defined functional domain hotspot threshold is met.
PM2	Met	This variant is extremely rare in population databases. It is absent from gnomAD v2.1 and gnomAD-Canada v1.0. In gnomAD v4.1, it is present at an allele frequency of 2.48e-6 (4/1,614,058 alleles, 0 homozygotes; grpmax FAF=7.9e-7), which is well below the 0.1% threshold for PM2. Highest subpopulation frequency is European (non-Finnish) at 3.39e-6.	gnomad_v2 gnomad_v4 gnomad_canada
PM3	N/A	Skipped per assessment instructions.
PM4	N/A	PM4 applies to in-frame insertions/deletions in non-repeat regions. This variant is a frameshift duplication and is assessed under PVS1; PM4 is not applicable.
PM5	N/A	PM5 requires a same-residue missense comparator with an established pathogenic classification. This frameshift variant does not have a classic missense comparator, and the automated PM5 candidate harvest confirmed no eligible same-residue candidates.	pm5_candidates
PM6	Not assessed	No de novo data are available for this variant.
PP1	Not assessed	No segregation data are available for this variant.
PP2	N/A	PP2 applies to genes where missense variants are a predominant mechanism of disease with a low rate of benign missense variation. RAD50 is a gene where loss-of-function (truncating) variants are the primary disease mechanism; PP2 is not applicable.
PP3	N/A	PP3 relies on multiple lines of in silico evidence (REVEL, BayesDel, splicing predictors) supporting a deleterious effect. REVEL and BayesDel are not available for non-SNV frameshift variants. SpliceAI max delta is 0.02, indicating no significant splicing impact. PP3 is not applicable for this frameshift variant.	spliceai
PP4	Not assessed	Insufficient phenotype-level specificity data for the probands carrying this variant. While RAD50 deficiency is associated with NBS-like disorder, specific phenotype data for individuals with c.2033_2034dup are not available.
PP5	Met	This variant has been classified as Pathogenic in ClinVar by two independent clinical laboratories (Ambry Genetics and Labcorp Genetics/Invitae) using clinical testing criteria. Although the review status is criteria provided, single submitter (each), the consistent Pathogenic call from multiple clinical laboratories supports PP5 at the supporting level under generic ACMG/AMP.	clinvar
BA1	Not met	The variant allele frequency in gnomAD v4.1 is 2.48e-6 (0.00025%), far below the BA1 threshold of 1%.	gnomad_v4
BS1	Not met	The variant allele frequency of 2.48e-6 in gnomAD v4.1 is far below the BS1 threshold of 0.3%.	gnomad_v4
BS2	Not assessed	No data on observation of this variant in healthy adults, particularly in homozygous state, are available.
BS3	Not assessed	No variant-specific functional studies demonstrating no deleterious effect have been identified. The literature review returned gene-level studies but none examined this specific variant for benign functional outcome.
BS4	Not assessed	No segregation data are available to assess lack of cosegregation with disease.
BP1	N/A	BP1 applies to genes where a specific missense variant is observed when truncating variants are the only known cause of disease. RAD50 disease is caused by loss-of-function variants (truncating, frameshift, nonsense); a frameshift variant does not meet BP1 applicability criteria.
BP2	Not assessed	No data on observation of this variant in trans with a known pathogenic variant are available.
BP3	N/A	BP3 applies to in-frame indels in repetitive regions without a known function. This variant is a frameshift duplication and is not applicable for BP3.
BP4	N/A	BP4 relies on multiple lines of in silico evidence predicting no impact. REVEL and BayesDel are not available for non-SNV frameshift variants. SpliceAI shows no significant splicing impact (max delta=0.02), but BP4 is not designed for frameshift variants and is not applicable.	spliceai
BP5	Not met	BP5 applies when a variant is found in a case with an alternate molecular basis for disease. This variant has been observed in the context of RAD50-related disease (ClinVar Pathogenic classification) and no alternate molecular basis has been identified.
BP6	Not met	No reputable source has classified this variant as benign or likely benign. ClinVar classification is Pathogenic.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splicing impact. This is a frameshift variant; BP7 is not applicable.

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