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RAD50
Final classification
Likely Benign
RAD50 c.221A>C · p.Gln74Pro
RAD50

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.

Gene
RAD50
Transcript
NM_005732.3
HGVS · transcript:coding
NM_005732.3:c.221A>C
Consequence
N/A
GRCh38
chr5:132575784 A>C
GRCh37
chr5:131911476 A>C
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: PM2 moderate, BP1 supporting benign, BP4 supporting benign; combination = 1 moderate + 2 supporting benign, which maps to Likely Benign.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate, BP1 supporting benign, BP4 supporting benign; combination = 1 moderate + 2 supporting benign, which maps to Likely Benign.
Classification rationale
PM2 BP1BP4 Likely Benign
RAD50 c.221A>C

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.1 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.2 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.3 As a missense variant in a gene where truncating variants are the established disease mechanism, BP1 applies at supporting benign strength.4 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.5 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.6 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.7

PM2 + BP1 + BP4 Likely Benign
1 pvs1_gene_context
3 revelbayesdelspliceai ↗
4 pvs1_gene_context
7 generic_acmg_combination_rules
Gene diagram · NM_005732.3 · variants mapped to exon structure
RAD50 NM_005732.3
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 20 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
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 v2.1: 0 alleles (absent). gnomAD v4.1: 3 alleles total (AF=1.88e-6)all in NFE subpopulation (AF=2.58e-6)0 homozygotes
BP1 supporting Benign
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.
RAD50 germline disease mechanism is loss-of-function. PVS1 gene context confirmed LoF as the established mechanism via literature supporting biallelic null variants in RAD50 deficiency.
BP4 supporting Benign
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: 0.263 (no deleterious prediction). BayesDel: -0.354 (benign). SpliceAI: max delta 0.01 (no splice impact).
Assessed · not applied
Pathogenic
PS1 No alternate nucleotide change at c.221 resulting in the same amino acid change (p.Gln74Pro) has been established as pathogenic.
PS2 No de novo occurrence data available for this variant.
PS3 No variant-specific experimental functional data identified.
PS4 No case-control data demonstrating statistically significant enrichment of this variant in affected individuals.
PM1 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.
PM5 No pathogenic missense variant at amino acid position 74 with a different amino acid change was identified.
PM6 No de novo report available for this variant.
PP1 No co-segregation data available.
PP2 RAD50 disease (RAD50 deficiency, OMIM #613078) is primarily caused by biallelic loss-of-function variants.
PP3 Multiple lines of computational evidence suggest no damaging effect.
PP4 No patient phenotype or family history data available for review.
PP5 ClinVar reports this variant as Uncertain Significance (2 clinical laboratories), not pathogenic.
Benign
BA1 The variant allele frequency in gnomAD v4.1 is 0.000019% (3/1,594,676 alleles), far below the 1% BA1 threshold.
BS1 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.
BS2 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.
BS3 No well-established in vitro or in vivo functional studies demonstrate that this variant has no damaging effect on protein function or splicing.
BS4 No segregation data available showing lack of co-segregation with disease in affected family members.
BP2 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.
BP5 No observation of this variant in a case where an alternate molecular basis for disease has been identified.
BP6 ClinVar reports this variant as Uncertain Significance (2 clinical laboratories), not benign or likely benign.
N/A · 2 PVS1 · BP7
Research & evidence
Population frequency · supports benign
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= 1.88126e-06; MAF= 0.00019%, 3/1594676 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.58112e-06; MAF= 0.00026%, 3/1162284 alleles, homozygotes = 0); grpmax FAF= 6.9e-07.
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
0.00019% · 3 / 1,594,676
0 hom · FAF 6.9e-05%
European (non-Finnish)
3 / 1,162,284
0.00026%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
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 (2 clinical laboratories). (ClinVarID = 1053169)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.263. BayesDel score = -0.354261.
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. RAD50 encodes a component of protein complex critical to DNA double-stranded-break end processing. Select germline mutations of RAD50 predispose to br
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 not previously been reported in somatic cancers (COSMIC).
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 · 1 PMID not cited in assessment
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