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.2653T>C · p.Ser885Pro
AR

NM_000044.4:c.2653T>C (p.Ser885Pro) is a missense variant in exon 8 of AR, encoding the androgen receptor. This variant is absent from gnomAD population databases (v2.1, v4.1, Canada v1.0), meeting PM2 at moderate strength.

Gene
AR
Transcript
NM_000044.4
HGVS · transcript:coding
NM_000044.4:c.2653T>C
Consequence
N/A
GRCh38
chrX:67723731 T>C
GRCh37
chrX:66943573 T>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: PM1 supporting, PM2 moderate, BP4 supporting; combination = 1 moderate + 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: PM1 supporting, PM2 moderate, BP4 supporting; combination = 1 moderate + 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM1PM2 BP4 VUS
AR c.2653T>C

NM_000044.4:c.2653T>C (p.Ser885Pro) is a missense variant in exon 8 of AR, encoding the androgen receptor. This variant is absent from gnomAD population databases (v2.1, v4.1, Canada v1.0), meeting PM2 at moderate strength.1 The variant is located within the AR ligand-binding domain (residues ~671-919), a well-established critical functional domain where missense variants are a known cause of androgen insensitivity syndrome, meeting PM1 at supporting strength. Multiple computational predictors suggest no significant impact: SpliceAI delta score is 0.00 and BayesDel score is 0.335 (intermediate, not damaging), meeting BP4 at supporting strength.2 The variant is classified as Uncertain significance in ClinVar (VariationID 1410073) by a single clinical laboratory (Labcorp Genetics/Invitae) with review status 'criteria provided, single submitter'. No expert panel classification is available.3 No functional studies, case-control data, segregation data, de novo reports, or variant-specific publications were identified for this variant. OncoKB reports Unknown Oncogenic Effect with no curated functional evidence.4 Applying the generic ACMG/AMP 2015 classification rules (Richards et al. 2015, PMID:25741868): PM2 (moderate) + PM1 (supporting) + BP4 (supporting benign) yields conflicting evidence insufficient to classify as Likely Pathogenic or Likely Benign. The overall classification is Variant of Uncertain Significance (VUS).5

PM1 + PM2 + BP4 VUS
2 spliceai ↗bayesdel
5 generic_acmg_combination_rules
Gene diagram · NM_000044.4 · variants mapped to exon structure
AR NM_000044.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 18 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM1 supporting Pathogenic
p.Ser885Pro is located in the androgen receptor ligand-binding domain (LBD, residues ~671-919), a well-established critical functional domain where missense variants are a known cause of androgen insensitivity syndrome. The variant is absent from gnomAD population databases. However, position 885 is not a statistically significant mutational hotspot per cancerhotspots.org, and the residue has not been individually characterized as critical in functional studies. Domain-level PM1 applies at supporting strength.
Located in AR ligand-binding domain (residues ~671-919)a critical functional domainAbsent from gnomAD v2.1 and v4.1 — no benign variation at this position
PM2 moderate Pathogenic
NM_000044.4:c.2653T>C is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, meeting the PM2 threshold for a variant absent from large population databases (allele frequency < 0.1%).
Absent from gnomAD v2.1Absent from gnomAD v4.1Absent from gnomAD-Canada v1.0
BP4 supporting Benign
Multiple lines of computational evidence suggest no significant impact on the gene product. SpliceAI predicts no splicing alteration (max delta score = 0.00 across all categories). BayesDel score of 0.335 falls in the intermediate range and does not support a damaging prediction. REVEL is unavailable for this variant. The absence of any computational predictor suggesting a deleterious effect supports BP4 at supporting strength.
SpliceAI max delta = 0.00 — no predicted splice alterationBayesDel = 0.335 — intermediatenot in damaging range
Assessed · not applied
Pathogenic
PS2 No de novo observation has been reported for NM_000044.4:c.2653T>C.
PS3 No variant-specific functional studies exist for p.Ser885P.
PS4 No case-control data or statistical enrichment in affected individuals versus controls is available.
PM6 No de novo observation with confirmed maternity and paternity has been reported for this variant.
PP1 No segregation data is available for this variant.
PP2 PP2 requires demonstration that the gene has a low rate of benign missense variation and that missense variants are a common mechanism of disease.
PP3 Multiple lines of computational evidence do not support a deleterious effect.
PP4 No proband phenotype or family history information is available for this case.
PP5 The ClinVar entry for this variant (VariationID 1410073) is classified as Uncertain significance with review status 'criteria provided, single submitter' (1-star).
Benign
BA1 The variant is absent from all population databases (gnomAD v2.1, v4.1, Canada v1.0).
BS1 The variant is absent from gnomAD population databases.
BS2 No observation of this variant in a healthy adult individual has been reported for a disorder expected to have full penetrance at an early age.
BS3 No well-established functional studies demonstrating no damaging effect exist for this variant.
BS4 No segregation data is available to evaluate lack of segregation in affected family members.
BP1 BP1 applies to missense variants in genes where primarily truncating variants cause disease.
BP2 No observation of this variant in trans with a pathogenic variant has been reported.
BP5 No observation of this variant in a case with an alternate molecular basis for disease has been reported.
BP6 The ClinVar entry for this variant (VariationID 1410073) is classified as Uncertain significance, not Benign/Likely Benign.
N/A · 7 PVS1 · PS1 · PM3 · PM4 · PM5 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
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
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 = 1410073)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = 0.335265.
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 · 2 PMIDs not cited in assessment
20301508 ↗ Spinal and Bulbar Muscular Atrophy. CLINVAR
20301602 ↗ Androgen Insensitivity Syndrome. CLINVAR