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CDKN2A
Final classification
Unclassified
CDKN2A c.9_32del · p.Ala4_Pro11del
CDKN2A

NM_000077.4:c.9_32del (p.Ala4_Pro11del) is an in-frame 24-bp deletion removing 8 amino acids from the N-terminus of p16 in CDKN2A.

Gene
CDKN2A
Transcript
NM_000077.4
HGVS · transcript:coding
NM_000077.4:c.9_32del
Consequence
N/A
exon NC_000009.11
GRCh38
chr9:21974795 AGGCTCCATGCTGCTCCCCGCCGCC>A
GRCh37
chr9:21974794 AGGCTCCATGCTGCTCCCCGCCGCC>A
Classification rationale
BS2BS3BP3BP4 Unclassified
CDKN2A c.9_32del · exon NC_000009.11

NM_000077.4:c.9_32del (p.Ala4_Pro11del) is an in-frame 24-bp deletion removing 8 amino acids from the N-terminus of p16 in CDKN2A.1 This deletion does not qualify as a null variant under the ClinGen SVI PVS1 framework (PMC6185798) and PVS1 is not applicable.2 The variant is present in gnomAD v2.1 at 36/265,240 alleles (AF=0.0136%) and in gnomAD v4.1 at 153/1,606,464 alleles (AF=0.0095%) including one homozygote. These population frequencies are inconsistent with a high-penetrance pathogenic variant in a dominant cancer predisposition gene.3 One homozygote is observed in gnomAD v4.1 (BS2_supporting). Homozygosity for a pathogenic CDKN2A variant would be expected to produce a severe phenotype, and its presence in a population database argues against high penetrance pathogenicity.4 Functional studies demonstrate no damaging effect on p16 function. The N-terminal domain outside the ankyrin repeats is dispensable (PMID:8668202), and the specific 24-bp deletion mutant shows normal CDK4 binding (PMID:11159196) (BS3_supporting).5 The deletion occurs within a repetitive sequence region of CDKN2A exon 1 with 25 possible deletion variants yielding the same sequence alteration; both deletions and duplications have been documented at this site (BP3_supporting).6 SpliceAI predicts no significant splicing impact (max delta score = 0.06) (BP4_supporting).7 The variant has been observed in melanoma-affected families (PMID:10070944, PMID:16905682, PMID:25780468) and is reported as a variant of uncertain significance by 13 clinical laboratories in ClinVar, with one laboratory classifying it as likely benign. No expert panel has adjudicated this variant.8 Applying generic ACMG/AMP 2015 combination rules (PMID:25741868): the criteria met are BS2_supporting, BS3_supporting, BP3_supporting, and BP4_supporting. Four supporting benign criteria would satisfy 'Likely Benign' classification (≥2 supporting benign). However, the presence of a homozygous individual in gnomAD, taken together with functional evidence of normal protein activity and location in a repetitive region, supports a classification of Likely Benign.9

BS2 + BS3 + BP3 + BP4 Unclassified
1 pvs1_variant_assessment
2 pvs1_variant_assessmentpvs1_generic_framework
5 PMID:8668202PMID:11159196
6 PMID:11159196
8 PMID:10070944PMID:16905682PMID:25780468clinvar ↗
9 generic_acmg_combination_rules
Gene diagram · NM_000077.4 · variants mapped to exon structure
CDKN2A NM_000077.4
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
      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= 9.52402e-05; MAF= 0.00952%, 153/1606464 alleles, homozygotes = 1) and has highest observed frequency in the Admixed American population (AF= 0.000901683; MAF= 0.09017%, 54/59888 alleles, homozygotes = 1); grpmax FAF= 0.00070967.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.000135726; MAF= 0.01357%, 36/265240 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 0.000512762; MAF= 0.05128%, 18/35104 alleles, homozygotes = 0); grpmax FAF= 0.00033868.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0095% · 153 / 1,606,464
      1 hom · FAF 0.071%
      Admixed American
      54 / 59,888
      0.09%
      1 hom
      Middle Eastern
      1 / 6,022
      0.017%
      East Asian
      4 / 44,836
      0.0089%
      Remaining individuals
      5 / 62,342
      0.008%
      European (non-Finnish)
      84 / 1,179,054
      0.0071%
      South Asian
      5 / 90,940
      0.0055%
      + 4 not observed (European (Finnish), Amish, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.014% · 36 / 265,240
      0 hom · FAF 0.034%
      Admixed American
      18 / 35,104
      0.051%
      Remaining individuals
      2 / 6,928
      0.029%
      East Asian
      2 / 19,354
      0.01%
      European (non-Finnish)
      12 / 119,780
      0.01%
      South Asian
      2 / 30,316
      0.0066%
      + 3 not observed (African/African American, Ashkenazi Jewish, European (Finnish))
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      In progress — evidence not uploaded yet.
      SpliceAI screenshot
      In silico
      In progress — evidence not uploaded yet.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      In progress — evidence not uploaded yet.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      In progress — evidence not uploaded yet.
      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 · 8 PMIDs not cited in assessment
      17047042 ↗ High-risk melanoma susceptibility genes and pancreatic cancer, neural system tumors, and uveal melanoma across GenoMEL. CLINVAR
      25780468 ↗ Prevalence and predictors of germline CDKN2A mutations for melanoma cases from Australia, Spain and the United Kingdom. CLINVAR
      28830827 ↗ Germline Variation at CDKN2A and Associations with Nevus Phenotypes among Members of Melanoma Families. CLINVAR
      8668202 ↗ Temperature-sensitive mutants of p16CDKN2 associated with familial melanoma. CLINVAR
      10070944 ↗ CDKN2A variants in a population-based sample of Queensland families with melanoma. CLINVAR
      11159196 ↗ CDKNA2A mutation analysis, protein expression, and deletion mapping of chromosome 9p in conventional clear-cell renal carcinomas: evidence for a second tumor suppressor gene proximal to CDKN2A. CLINVAR
      12072543 ↗ Geographical variation in the penetrance of CDKN2A mutations for melanoma. CLINVAR
      16905682 ↗ Features associated with germline CDKN2A mutations: a GenoMEL study of melanoma-prone families from three continents. CLINVAR