Starting
Initialising…
0%
CYP21A2
Final classification
Likely Benign
CYP21A2 c.1439G>T · p.Arg480Leu
CYP21A2

NM_000500.9:c.1439G>T (p.Arg480Leu) is a missense variant in exon 10 of CYP21A2, a gene associated with autosomal recessive congenital adrenal hyperplasia due to 21-hydroxylase deficiency.

Gene
CYP21A2
Transcript
NM_000500.9
HGVS · transcript:coding
NM_000500.9:c.1439G>T
Consequence
N/A
GRCh38
chr6:32041085 G>T
GRCh37
chr6:32008862 G>T
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: PS3 supporting, BS1 supporting benign, BP4 supporting benign, BP6 supporting benign; combination = 1 supporting + 3 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: PS3 supporting, BS1 supporting benign, BP4 supporting benign, BP6 supporting benign; combination = 1 supporting + 3 supporting benign, which maps to Likely Benign.
Classification rationale
PS3 BS1BP4BP6 Likely Benign
CYP21A2 c.1439G>T

NM_000500.9:c.1439G>T (p.Arg480Leu) is a missense variant in exon 10 of CYP21A2, a gene associated with autosomal recessive congenital adrenal hyperplasia due to 21-hydroxylase deficiency. The variant is present in gnomAD at an appreciable global allele frequency of 0.62% (v2.1, 1521/244182 alleles) and 0.33% (v4.1, 5128/1571116 alleles), exceeding the BS1 threshold (>0.3%) for a recessive disorder.1 In silico predictions are uniformly benign: REVEL score 0.334, BayesDel score -0.316 (predicting benign), and SpliceAI detects no splice alteration (max delta 0.00), satisfying BP4.2 ClinVar reports this variant as Benign by three clinical laboratories and Likely benign by three additional laboratories, with two VUS submissions, supporting BP6.3 Functional studies demonstrate the variant retains ~75-80% of wild-type 21-hydroxylase activity in transfected COS-1 cells, consistent with a mild functional impact, providing PS3 at the supporting level.4 Applying the generic ACMG/AMP 2015 combination rules (PMID:25741868), the criteria met are three supporting benign (BS1, BP4, BP6) and one supporting pathogenic (PS3). Likely benign requires at least two supporting benign criteria, which is satisfied.5

PS3 + BS1 + BP4 + BP6 Likely Benign
2 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_000500.9 · variants mapped to exon structure
CYP21A2 NM_000500.9
Fetching transcript structure from UCSC…
Applied criteria · 4 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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= 0.00326392; MAF= 0.32639%, 5128/1571116 alleles, homozygotes = 1) and has highest observed frequency in the African/African American population (AF= 0.0586541; MAF= 5.86541%, 4316/73584 alleles, homozygotes = 1); grpmax FAF= 0.0571923.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.00622896; MAF= 0.62290%, 1521/244182 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.0607908; MAF= 6.07908%, 1316/21648 alleles, homozygotes = 0); grpmax FAF= 0.0615449.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.33% · 5128 / 1,571,116
      1 hom · FAF 5.7%
      African/African American
      4316 / 73,584
      5.9%
      1 hom
      Middle Eastern
      25 / 4,656
      0.54%
      Admixed American
      308 / 58,074
      0.53%
      Remaining individuals
      305 / 61,106
      0.5%
      South Asian
      50 / 88,918
      0.056%
      European (non-Finnish)
      124 / 1,159,074
      0.011%
      + 4 not observed (European (Finnish), Amish, East Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.62% · 1521 / 244,182
      0 hom · FAF 6.2%
      African/African American
      1316 / 21,648
      6.1%
      Admixed American
      140 / 33,094
      0.42%
      Remaining individuals
      17 / 6,458
      0.26%
      South Asian
      20 / 28,606
      0.07%
      European (non-Finnish)
      28 / 111,522
      0.025%
      + 3 not observed (Ashkenazi Jewish, East Asian, European (Finnish))
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Benign (3 clinical laboratories) and as Uncertain significance (2 clinical laboratories) and as Likely benign (1 clinical laboratory) and as likely benign (1 clinical laboratory) and as Likely Benign (1 clinical laboratory). (ClinVarID = 445854)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.334. BayesDel score = -0.315808.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      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 previously been reported in somatic cancers (COSMIC; COSV99056687, n = 3 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      2papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 6 further PMIDs triaged but not cited — see Sources & References.
      Characterization of novel missense mutations in CYP21 causing congenital adrenal hyperplasia.
      Found
      (Robins et al.
      Applied to
      PS3 supports · met
      Linkage analysis of the C4A/C4B copy number variation and polymorphisms of the adjacent steroid 21-hydroxylase gene in a healthy population.
      Found
      gnomAD v2.1 global AF: 0.62% gnomAD v4.1 global AF: 0.33% PMID:19505723: R479L found in 1/92 healthy Hungarian individuals
      Applied to
      BS1 supports · met
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 6 PMIDs not cited in assessment
      15110320 ↗ Detection and assignment of CYP21 mutations using peptide mass signature genotyping. CLINVAR
      16788163 ↗ Molecular model of human CYP21 based on mammalian CYP2C5: structural features correlate with clinical severity of mutations causing congenital adrenal hyperplasia. CLINVAR
      21169732 ↗ A large view of CYP21 locus among Sicilians and other populations: identification of a novel CYP21A2 variant in Sicily. CLINVAR
      21228398 ↗ Carrier testing for severe childhood recessive diseases by next-generation sequencing. CLINVAR
      23241443 ↗ Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene. CLINVAR
      23359706 ↗ Structure-phenotype correlations of human CYP21A2 mutations in congenital adrenal hyperplasia. CLINVAR