Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
AR
Final classification
VUS
AR c.59G>A · p.Arg20Gln
AR

This variant is absent from gnomAD v2.1 and gnomAD-Canada, and present at extremely low frequency in gnomAD v4.1 (1/1,206,311 alleles, AF 8.29e-07), meeting PM2 at supporting level.

Gene
AR
Transcript
NM_000044.4
HGVS · transcript:coding
NM_000044.4:c.59G>A
Consequence
N/A
GRCh38
chrX:67545205 G>A
GRCh37
chrX:66765047 G>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: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, 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: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
AR c.59G>A

This variant is absent from gnomAD v2.1 and gnomAD-Canada, and present at extremely low frequency in gnomAD v4.1 (1/1,206,311 alleles, AF 8.29e-07), meeting PM2 at supporting level.1 Multiple lines of in silico evidence predict no deleterious effect: SpliceAI max delta = 0.02 (no splicing impact) and BayesDel score = 0.226 (below pathogenic threshold), meeting BP4 at supporting benign level.2 PVS1 is not applicable as this is a missense variant (p.Arg20Gln), not a predicted null variant.3 No functional data, case-control studies, segregation data, or variant-specific publications were identified. PS3, PS4, and PM1 are not met.4 ClinVar reports this variant as Uncertain significance (1 clinical laboratory, criteria provided). No expert panel classification is available.5 The available evidence is insufficient to classify this variant as pathogenic or benign. One supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4) are met, leaving the variant as a Variant of Uncertain Significance (VUS) under ACMG/AMP 2015 rules.6

PM2 + BP4 VUS
Gene diagram · NM_000044.4 · variants mapped to exon structure
AR NM_000044.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 9 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is extremely rare in population databases. In gnomAD v4.1, it is observed in 1 of 1,206,311 alleles (AF = 8.29e-07; 0.00008%), well below the PM2 threshold of 0.1%. It is absent from gnomAD v2.1 and gnomAD-Canada.
gnomAD v4.1: 1/1206311 alleles (AF 8.29e-07
BP4 supporting Benign
Multiple lines of computational evidence predict no deleterious effect. SpliceAI predicts no splicing impact (max delta = 0.02). BayesDel score = 0.226 is below the pathogenic range. These in silico findings are consistent with a benign impact.
SpliceAI: max delta = 0.02 (no predicted splice alteration)BayesDel: score = 0.225865 (below damaging threshold)
Assessed · not applied
Pathogenic
PS1 No same amino acid change (p.Arg20Gln) has been previously established as pathogenic independent of this variant.
PS3 No functional data exists for NM_000044.4:c.59G>A (p.Arg20Gln).
PS4 No case-control data or prevalence comparison between affected and unaffected individuals is available for this variant.
PM1 The variant (p.Arg20Gln) lies in the N-terminal transactivation domain of AR, but is not located in a statistically significant mutational hotspot per cancerhotspots.org, and no variant-specific or domain-level functional characterization from the available publications supports PM1 application for this residue.
PP2 AR does not meet the PP2 requirements.
PP3 Multiple lines of in silico evidence do not support a deleterious effect.
Benign
BA1 gnomAD v4.1 AF = 8.29e-07 (0.00008%) is far below the BA1 threshold of 1%.
BS1 gnomAD v4.1 AF = 8.29e-07 (0.00008%) is far below the BS1 threshold of 0.3%.
BS3 No functional data demonstrating absence of deleterious effect exists for this variant.
N/A · 14 PVS1 · PS2 · PM5 · PM6 · PP1 · PP4 · PP5 · BS2 · BS4 · BP1 · BP2 · BP5 · BP6 · 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= 8.28974e-07; MAF= 0.00008%, 1/1206311 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.11821e-06; MAF= 0.00011%, 1/894288 alleles, homozygotes = 0).
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
8.3e-05% · 1 / 1,206,311
0 hom
European (non-Finnish)
1 / 894,288
0.00011%
+ 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 (1 clinical laboratory). (ClinVarID = 4129409)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). BayesDel score = 0.225865.
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. AR (androgen receptor), a transcription factor, is most frequently altered in advanced or castration-resistant prostate cancer.
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 · 5 PMIDs not cited in assessment
23619275 ↗ ACMG position statement on prenatal/preconception expanded carrier screening. CLINVAR
25730230 ↗ Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine. CLINVAR
23037933 ↗ Including the initial newborn screening bloodspot collection device serial number on birth certificates: basis and recommendations from the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children. CLINVAR
24394680 ↗ Parental permission for pilot newborn screening research: guidelines from the NBSTRN. CLINVAR
31022120 ↗ ACOG Committee Opinion No. 778 Summary: Newborn Screening and the Role of the Obstetrician-Gynecologist. CLINVAR