9-21971033-G-T

Position:

• chr9-21971033-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_Moderate PM2

The NM_058195.4(CDKN2A):​c.369C>A​(p.Cys123*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,453,986 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: CDKN2A NM_058195.4 stop_gained
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:3
• Conservation: PhyloP100: 0.312

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 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0752 CDS is truncated, and there are 2 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKN2A	NM_058195.4	c.369C>A	p.Cys123*	stop_gained	2/3	ENST00000579755.2	NP_478102.2
CDKN2A	NM_000077.5	c.326C>A	p.Ala109Asp	missense_variant	2/3	ENST00000304494.10	NP_000068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKN2A	ENST00000579755.2	c.369C>A	p.Cys123*	stop_gained	2/3	1	NM_058195.4	ENSP00000462950.1
CDKN2A	ENST00000304494.10	c.326C>A	p.Ala109Asp	missense_variant	2/3	1	NM_000077.5	ENSP00000307101.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000422 AC: 1 AN: 236746 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 129768

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: 0.0000329

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000206 AC: 3 AN: 1453986 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 723582

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: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.00e-7

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000936 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Apr 21, 2016

This variant is denoted CDKN2A c.326C>A at the cDNA level and p.Ala109Asp (A109D) at the protein level using the primary, p16, transcript. The CDKN2A open reading frame encodes for at least two proteins; p16 and p14-ARF, the later expressed mainly under elevated mitogenic stimulation. This C>A substitution results in the change of an Alanine to an Aspartic Acid (GCC>GAC) in the p16 protein while in the p14-ARF protein it results in a nonsense variant, denoted as c.369C>A and p.Cys123Ter, which changes a Cysteine to a premature stop codon (TGT>TGA) causing the loss of the last 10 amino acids.CDKN2A Ala109Asp, in the p16 protein, has not, to our knowledge, been published in the literature as pathogenic or benign. This variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. Since Alanine and Aspartic Acid differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. CDKN2A Ala109Asp occurs at a position that is not conserved and is not located in a known functional domain (UniProt). In silico analyses are inconsistent regarding the effect this variant may have on protein structure and function. CDKN2A Cys123Ter, in the p14-ARF protein, is predicted to cause loss of normal function through protein truncation; however, the protein is not expected to undergo nonsense-mediated decay. Therefore the resultant protein may retain some normal function. In summary, based on currently available evidence, both the amino acid substitution in the p16 protein, Ala109Asp, and the nonsense change in the p14-ARF protein, Cys123Ter, are considered variants of uncertain significance. -

Hereditary cancer-predisposing syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 17, 2024

The p.A109D variant (also known as c.326C>A), located in coding exon 2 of the CDKN2A gene, results from a C to A substitution at nucleotide position 326. The alanine at codon 109 is replaced by aspartic acid, an amino acid with dissimilar properties. This alteration performed similar to wild type in a cell cycle arrest assay (Miller PJ et al. Hum. Mutat., 2011 Aug;32:900-11). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Familial melanoma Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 06, 2023

The CDKN2A gene encodes two different proteins, p16INK4a and p14ARF, which are translated from alternative transcripts with different open reading frames. Both transcripts have been analyzed. We report either the variant with the higher classification or default to the CDKN2A (p16INK4a) variant. This report therefore includes the details for the CDKN2A (p16INK4a) variant. This sequence change replaces alanine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 109 of the CDKN2A (p16INK4a) protein (p.Ala109Asp). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CDKN2A (p16INK4a)-related conditions. This variant is also known as c.369C>A (p.Cys123*) in the CDKN2A (p14ARF) transcript. ClinVar contains an entry for this variant (Variation ID: 420995). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Experimental studies have shown that this missense change does not substantially affect CDKN2A (p16INK4a) function (PMID: 12606942). 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	Uncertain	0.46
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Uncertain	0.050
CADD	Benign	17
DANN	Uncertain	0.99
DEOGEN2	Benign	0.18	T;T;.;.;.;.;T;.
Eigen	Benign	-0.38
Eigen_PC	Benign	-0.40
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.63	T;T;.;T;.;T;T;T
MetaRNN	Uncertain	0.58	D;D;D;D;D;D;D;D
MetaSVM	Benign	-0.97	T
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-2.3	N;.;.;N;.;.;.;.
REVEL	Uncertain	0.60
Sift	Benign	0.39	T;.;.;T;.;.;.;.
Sift4G	Benign	0.39	T;T;T;T;T;T;T;T
Polyphen		1.0	D;.;.;.;.;.;.;.
Vest4		0.35
MutPred		0.48		Loss of MoRF binding (P = 0.0323);Loss of MoRF binding (P = 0.0323);.;Loss of MoRF binding (P = 0.0323);.;.;.;.;
MVP		0.99
MPC		0.68
ClinPred		0.27	T
GERP RS		3.1
Varity_R		0.19
gMVP		0.66

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: rs1064794838; hg19: chr9-21971032;