rs786201539

Positions:

• chr9-21970934-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1 BP4_Moderate BS2

The NM_000077.5(CDKN2A):​c.425A>G​(p.His142Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,612,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H142D) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000016 (0 hom.)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:6
• Conservation: PhyloP100: -1.13

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM1: In a chain Cyclin-dependent kinase inhibitor 2A (size 155) in uniprot entity CDN2A_HUMAN there are 119 pathogenic changes around while only 33 benign (78%) in NM_000077.5
• BP4: Computational evidence support a benign effect (MetaRNN=0.070082694).
• BS2: High AC in GnomAdExome4 at 23 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDKN2A	NM_000077.5	c.425A>G	p.His142Arg	missense_variant	2/3	ENST00000304494.10
CDKN2A	NM_058195.4	c.*69A>G		3_prime_UTR_variant	2/3	ENST00000579755.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKN2A	ENST00000304494.10	c.425A>G	p.His142Arg	missense_variant	2/3	1	NM_000077.5	P2
CDKN2A	ENST00000579755.2	c.*69A>G		3_prime_UTR_variant	2/3	1	NM_058195.4

Frequencies

GnomAD3 genomes AF: 0.0000131 AC: 2 AN: 152238 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000121 AC: 3 AN: 246972 Hom.: 0 AF XY: 0.00000746 AC XY: 1 AN XY: 134132

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000271

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000158 AC: 23 AN: 1460164 Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15 AN XY: 726462

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000207

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000131 AC: 2 AN: 152238 Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2 AN XY: 74384

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000282 Hom.: 0

Bravo AF: 0.0000113

ExAC AF: 0.0000165 AC: 2

EpiCase AF: 0.000164

EpiControl AF: 0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Aug 23, 2022	This missense variant replaces histidine with arginine at codon 142 of the CDKN2A protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Functional studies have shown that this variant impairs protein interaction with the binding partners, leukemogenic potential, and CDK4/6 inhibitory function of the CDKN2A protein (PMID: 20522552, 28218424, 34369425). Most of the variant effect on protein function was reported to be mild. This variant has been reported in four individuals affected with melanoma (PMID: 18983535, 19158841, 21462282) and in an individual affected with acute lymphoblastic leukemia (PMID: 26104880). One of the individuals affected with melanoma was reported to carry a pathogenic variant in the same gene (PMID: 18983535). This variant has been identified in 3/246972 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Uncertain significance, no assertion criteria provided	clinical testing	True Health Diagnostics	Apr 06, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Feb 07, 2023	The p.H142R variant (also known as c.425A>G), located in coding exon 2 of the CDKN2A gene, results from an A to G substitution at nucleotide position 425. The histidine at codon 142 is replaced by arginine, an amino acid with highly similar properties. This variant was previously detected as a germline alteration in a patient with multiple melanomas, who also harbored a pathogenic CDKN2A mutation and in an unrelated sporadic single melanoma patient (Pastorino et al. Pigment Cell Melanoma Res. 2008 Dec;21:700-9). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

not provided Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Mar 18, 2022	The CDKN2A c.425A>G; p.His142Arg variant (rs759922342) is reported in the literature in individuals affected with melanoma or acute lymphoblastic leukemia (Daniotti 2009, Miller 2011, Pastorino 2008, Xu 2015). However, at least one affected individual carrying this variant also carried a known pathogenic variant in CDKN2A (Pastorino 2008). The p.His142Arg variant is found on three chromosomes (3/246972 alleles) in the Genome Aggregation Database. The histidine at codon 142 is weakly conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.441). However, functional studies of the variant protein suggest reduced tumor suppressor activity (Li 2022) and reduced interaction with binding partner proteins (Sun 2010). Due to conflicting information, the clinical significance of the p.His142Arg variant is uncertain at this time. References: Daniotti et al. Cutaneous melanoma in childhood and adolescence shows frequent loss of INK4A and gain of KIT. J Invest Dermatol. 2009; 129(7): 1759-1768. PMID: 19158841. Li C et al. The functional role of inherited CDKN2A variants in childhood acute lymphoblastic leukemia. Pharmacogenet Genomics. 2022 Feb 1;32(2):43-50. PMID: 34369425. Miller et al. Classifying variants of CDKN2A using computational and laboratory studies. Hum Mutat. 2011; 32(8): 900-911. PMID: 21462282. Pastorino et al. CDKN2A mutations and MC1R variants in Italian patients with single or multiple primary melanoma. Pigment Cell Melanoma Res. 2008; 21(6): 700-709. PMID: 18983535. Sun et al. GRIM-19 and p16(INK4a) synergistically regulate cell cycle progression and E2F1-responsive gene expression. J Biol Chem. 2010; 285(36): 27545-27552. PMID: 20522552. Xu et al. Inherited coding variants at the CDKN2A locus influence susceptibility to acute lymphoblastic leukaemia in children. Nat Commun. 2015; 6:7553. PMID: 26104880. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Sep 20, 2023	Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Observed in individuals with melanoma; however, one of these individuals also harbored a pathogenic CDKN2A variant, as well as in individual(s) with leukemia (Pastorino et al., 2008; Daniotti et al., 2009; Xu et al., 2015; Vergani et al., 2021; Li et al., 2022); This variant is associated with the following publications: (PMID: 26104880, 21462282, 8834170, 18983535, 9132280, 19158841, 21619050, 20522552, 34573422, 34426522, 34369425) -

Familial melanoma Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 142 of the CDKN2A (p16INK4a) protein (p.His142Arg). This variant is present in population databases (rs759922342, gnomAD 0.002%). This missense change has been observed in individual(s) with acute lymphoblastic leukemia and/or melanoma (PMID: 18983535, 19158841, 21462282, 26104880). ClinVar contains an entry for this variant (Variation ID: 184564). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The arginine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Experimental studies have shown that this missense change affects CDKN2A (p16INK4a) function (PMID: 20522552, 34369425). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.072
BayesDel_addAF	Benign	-0.024	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	0.26
DANN	Benign	0.38
DEOGEN2	Benign	0.087	T;.;.;.;.;T;.
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.8
FATHMM_MKL	Benign	0.068	N
LIST_S2	Benign	0.51	T;.;T;.;T;T;T
M_CAP	Benign	0.046	D
MetaRNN	Benign	0.070	T;T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationTaster	Benign	1.0	N;N;N;N;N;N;N;N;N;N;N;N
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-0.67	N;.;N;.;.;.;.
REVEL	Uncertain	0.44
Sift	Benign	0.058	T;.;T;.;.;.;.
Sift4G	Benign	0.69	T;T;T;T;T;T;T
Polyphen		0.0	B;.;.;.;.;.;.
Vest4		0.26
MutPred		0.43		Gain of MoRF binding (P = 0.0165);.;Gain of MoRF binding (P = 0.0165);.;.;.;.;
MVP		0.60
MPC		0.50
ClinPred		0.050	T
GERP RS		-6.6
Varity_R		0.049
gMVP		0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs759922342; hg19: chr9-21970933;