9-21974733-A-G

Variant names:

• chr9-21974733-A-G
• rs878853650
• NM_000077.5:c.95T>C

Variant summary

Our verdict is Pathogenic. The variant received 13 ACMG points: 14P and 1B. PM1 PP3_Strong PP5_Very_Strong BS2_Supporting

The NM_000077.5(CDKN2A):​c.95T>C​(p.Leu32Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000411 in 1,460,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L32V) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 4.47
• Publications: 16 publications found

Genes affected

CDKN2A (HGNC:1787): (cyclin dependent kinase inhibitor 2A) This gene generates several transcript variants which differ in their first exons. At least three alternatively spliced variants encoding distinct proteins have been reported, two of which encode structurally related isoforms known to function as inhibitors of CDK4 kinase. The remaining transcript includes an alternate first exon located 20 Kb upstream of the remainder of the gene; this transcript contains an alternate open reading frame (ARF) that specifies a protein which is structurally unrelated to the products of the other variants. This ARF product functions as a stabilizer of the tumor suppressor protein p53 as it can interact with, and sequester, the E3 ubiquitin-protein ligase MDM2, a protein responsible for the degradation of p53. In spite of the structural and functional differences, the CDK inhibitor isoforms and the ARF product encoded by this gene, through the regulatory roles of CDK4 and p53 in cell cycle G1 progression, share a common functionality in cell cycle G1 control. This gene is frequently mutated or deleted in a wide variety of tumors, and is known to be an important tumor suppressor gene. [provided by RefSeq, Sep 2012]

CDKN2A Gene-Disease associations (from GenCC):

• melanoma, cutaneous malignant, susceptibility to, 2

  Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
• melanoma-pancreatic cancer syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
• familial atypical multiple mole melanoma syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• melanoma and neural system tumor syndrome

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000264545 (HGNC:):

ACMG classification

Our verdict: Pathogenic. The variant received 13 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 43 uncertain in NM_000077.5
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.972
• PP5: Variant 9-21974733-A-G is Pathogenic according to our data. Variant chr9-21974733-A-G is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 236992.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High AC in GnomAdExome4 at 6 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000077.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKN2A	NM_000077.5	MANE Select	c.95T>C	p.Leu32Pro	missense	Exon 1 of 3	NP_000068.1
	CDKN2A	NM_058195.4	MANE Plus Clinical	c.194-3525T>C		intron	N/A	NP_478102.2
	CDKN2A	NM_001195132.2		c.95T>C	p.Leu32Pro	missense	Exon 1 of 4	NP_001182061.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKN2A	ENST00000304494.10	TSL:1 MANE Select	c.95T>C	p.Leu32Pro	missense	Exon 1 of 3	ENSP00000307101.5
	CDKN2A	ENST00000498124.1	TSL:1	c.95T>C	p.Leu32Pro	missense	Exon 1 of 4	ENSP00000418915.1
	CDKN2A	ENST00000380151.3	TSL:1	n.95T>C		non_coding_transcript_exon	Exon 1 of 3	ENSP00000369496.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000411 AC: 6 AN: 1460584 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 726616

African (AFR) AF: 0.00 AC: 0 AN: 33476

American (AMR) AF: 0.00 AC: 0 AN: 44710

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26114

East Asian (EAS) AF: 0.00 AC: 0 AN: 39698

South Asian (SAS) AF: 0.00 AC: 0 AN: 86242

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52424

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000540 AC: 6 AN: 1111792

Other (OTH) AF: 0.00 AC: 0 AN: 60360

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Melanoma-pancreatic cancer syndrome Pathogenic:2

Aug 14, 2025

Myriad Genetics, Inc.

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 20340136]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 8595405, 11500805, 12072543, 16905682].

Jan 03, 2025

Molecular Pathology, Peter Maccallum Cancer Centre

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Familial melanoma Pathogenic:2

Aug 03, 2018

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: CDKN2A c.95T>C (p.Leu32Pro) results in a non-conservative amino acid change located in the Ankyrin repeat-containing domain (IPR020683) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 239900 control chromosomes (gnomAD). The variant, c.95T>C, has been reported in the literature in individuals affected with Cutaneous Malignant Melanoma (Jouenne_2016, Jovanovic_2010, Box_2001, McKenzie_2010). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (McKenzie_2010). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Mar 10, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has been reported in patients and families affected with melanoma and pancreatic cancer (PMID: 19759551, 17218939, 16905682, 20340136, 17047042, 28592523).  It has been shown to segregate with disease in one family (PMID: 8595405). ClinVar contains an entry for this variant (Variation ID: 236992). This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with proline at codon 32 of the CDKN2A (p16INK4a) protein (p.Leu32Pro). The leucine residue is moderately conserved and there is a moderate physicochemical difference between leucine and proline. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic Experimental studies have shown that this missense change interferes with the interaction between p16INK4a and its binding partners CDK4 and CDK6 (PMID: 20340136, 19712690).

not provided Pathogenic:1

Jun 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CDKN2A: PP1:Strong, PM2, PS4:Moderate, PS3:Supporting

Hereditary cancer-predisposing syndrome Pathogenic:1

May 27, 2024

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.L32P variant (also known as c.95T>C), located in coding exon 1 of the CDKN2A gene, results from a T to C substitution at nucleotide position 95. The leucine at codon 32 is replaced by proline, an amino acid with similar properties. This variant has been reported in numerous individuals with a personal and/or family history of cutaneous melanoma (Aitken J et al, J. Natl. Cancer Inst. 1999 Mar; 91(5):446-52; Box NF et al. Am J Hum Genet, 2001 Oct;69:765-73; Begg CB et al, J. Natl. Cancer Inst. 2005 Oct; 97(20):1507-15; Berwick M et al, Cancer Epidemiol. Biomarkers Prev. 2006 Aug; 15(8):1520-5; Bishop DT et al, J. Natl. Cancer Inst. 2002 Jun; 94(12):894-903; Goldstein AM et al, Cancer Res. 2006 Oct; 66(20):9818-28; Goldstein AM et al, J. Med. Genet. 2007 Feb; 44(2):99-10; Jovanovic B et al, J. Invest. Dermatol. 2010 Feb; 130(2):618-20; Orlow I et al, J. Invest. Dermatol. 2007 May; 127(5):1234-43; Jouenne F et al. J Med Genet, 2017 Sep;54:607-612; Taylor NJ et al. J Invest Dermatol, 2017 Dec;137:2606-2612). Further, a functional analysis of the p.L32P variant has demonstrated abolished CDK4 binding capability (McKenzie HA et al, Hum. Mutat. 2010 Jun; 31(6):692-701). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.94
BayesDel_addAF	Pathogenic	0.39	D
BayesDel_noAF	Pathogenic	0.32
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.68	D
Eigen	Pathogenic	0.92
Eigen_PC	Pathogenic	0.78
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.84	T
M_CAP	Pathogenic	0.89	D
MetaRNN	Pathogenic	0.97	D
MetaSVM	Uncertain	0.70	D
PhyloP100		4.5
PrimateAI	Uncertain	0.72	T
PROVEAN	Pathogenic	-5.7	D
REVEL	Pathogenic	0.80
Sift	Uncertain	0.0010	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.81
MutPred		0.74		Gain of disorder (P = 0.0175)
MVP		0.97
MPC		1.6
ClinPred		1.0	D
GERP RS		4.9
PromoterAI		0.012	Neutral
Varity_R		0.89
gMVP		1.0
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs878853650; hg19: chr9-21974732; COSMIC: COSV58685103; COSMIC: COSV58685103;