NM_000077.5:c.146T>C

Variant names:

• chr9-21974682-A-G
• rs199907548
• NM_000077.5:c.146T>C

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 9P and 6B. PS3 PM1 PM5 PP5 BP4 BS1_Supporting BS2

The NM_000077.5(CDKN2A):​c.146T>C​(p.Ile49Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00011 in 1,613,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). ClinVar reports functional evidence for this variant: "SCV000212740: Multiple functional studies have demonstrated that this variant diminishes the binding activity of p16 to CDK4 and CDK6 and displays reduced ability to affect Rb dephosphorylation, however the degree of effect is shown to be more intermediate than other known pathogenic variants (Ranade K et al. Nat. Genet. 1995 May;10:114-6; Reymond A et al. Oncogene. 1995 Sep;11:1173-8; Yang R et al. Biochem. Biophys. Res. Commun. 1996 Jan;218:254-9; Walker GJ et al. Int. J. Cancer. 1999 Jul;82:305-12). Cell cycle inhibition assays have demonstrated that this variant is functionally deleterious (Miller, PJ et al. Hum Mutat 2011 Aug;32(8):900-11; Kimura H et al. Elife 2022 Jan;11:).; SCV001339145: Multiple experimental studies showed conflicting results including: decreased inhibition of cyclinD1/CDK4 and cyclin D1/CDK6 activity (Ranade_1995), decreased binding activity to CDK4 (Yang_1996, Reymond_1995), no effect on binding to the kinases but substantially diminished ability to inhibit cell growth and mis-localization (Walker_1999), loss of function in a cell cycle arrest assay (Miller_2011) and most recently, cell cycle suppression that was similar to WT (Horn_2021). The following publications have been ascertained in the context of this evaluation (PMID:16234564, 27756164, 18335566, 27960642, 28765326, 33823155, 7987387, 9166859, 21462282, 16818274, 18519632, 31921681, 26681309, 7647780, 7566978, 28640387, 7718873, 30339520, 10389768, 8573142, 25980754).; SCV006298703: Functional studies indicate this variant impacts protein function [PMID:35001868, 10389768, 21462282].; SCV000805818: Functional studies have suggested that this variant may mildly impact enzyme function (Ranade et al. 1995. PubMed ID: 7647780; Walker et al. 1999. PubMed ID: 10389768).". Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I49M) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000072 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00011 (0 hom.)
• Consequence: CDKN2A NM_000077.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:7 U:10 O:1
• Conservation: PhyloP100: 5.56
• Publications: 40 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: Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, Genomics England PanelApp
• 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: Uncertain_significance. The variant received 3 ACMG points.

• PS3: PS3 evidence extracted from ClinVar submissions: SCV000212740: Multiple functional studies have demonstrated that this variant diminishes the binding activity of p16 to CDK4 and CDK6 and displays reduced ability to affect Rb dephosphorylation, however the degree of effect is shown to be more intermediate than other known pathogenic variants (Ranade K et al. Nat. Genet. 1995 May;10:114-6; Reymond A et al. Oncogene. 1995 Sep;11:1173-8; Yang R et al. Biochem. Biophys. Res. Commun. 1996 Jan;218:254-9; Walker GJ et al. Int. J. Cancer. 1999 Jul;82:305-12). Cell cycle inhibition assays have demonstrated that this variant is functionally deleterious (Miller, PJ et al. Hum Mutat 2011 Aug;32(8):900-11; Kimura H et al. Elife 2022 Jan;11:).; SCV001339145: Multiple experimental studies showed conflicting results including: decreased inhibition of cyclinD1/CDK4 and cyclin D1/CDK6 activity (Ranade_1995), decreased binding activity to CDK4 (Yang_1996, Reymond_1995), no effect on binding to the kinases but substantially diminished ability to inhibit cell growth and mis-localization (Walker_1999), loss of function in a cell cycle arrest assay (Miller_2011) and most recently, cell cycle suppression that was similar to WT (Horn_2021). The following publications have been ascertained in the context of this evaluation (PMID: 16234564, 27756164, 18335566, 27960642, 28765326, 33823155, 7987387, 9166859, 21462282, 16818274, 18519632, 31921681, 26681309, 7647780, 7566978, 28640387, 7718873, 30339520, 10389768, 8573142, 25980754).; SCV006298703: Functional studies indicate this variant impacts protein function [PMID: 35001868, 10389768, 21462282].; SCV000805818: Functional studies have suggested that this variant may mildly impact enzyme function (Ranade et al. 1995. PubMed ID: 7647780; Walker et al. 1999. PubMed ID: 10389768).
• PM1: In a hotspot region, there are 12 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 48 uncertain in NM_000077.5
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr9-21974682-A-C is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 430217.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP5: Variant 9-21974682-A-G is Pathogenic according to our data. Variant chr9-21974682-A-G is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 127523.
• BP4: Computational evidence support a benign effect (MetaRNN=0.063048065). . Strength limited to SUPPORTING due to the PP5.
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0000723 (11/152212) while in subpopulation AMR AF = 0.000654 (10/15292). AF 95% confidence interval is 0.000354. There are 0 homozygotes in GnomAd4. There are 9 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High AC in GnomAd4 at 11 AD gene.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKN2A	NM_000077.5	MANE Select	c.146T>C	p.Ile49Thr	missense	Exon 1 of 3	NP_000068.1	P42771-1
	CDKN2A	NM_058195.4	MANE Plus Clinical	c.194-3474T>C		intron	N/A	NP_478102.2	Q8N726-1
	CDKN2A	NM_001195132.2		c.146T>C	p.Ile49Thr	missense	Exon 1 of 4	NP_001182061.1	P42771-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKN2A	ENST00000304494.10	TSL:1 MANE Select	c.146T>C	p.Ile49Thr	missense	Exon 1 of 3	ENSP00000307101.5	P42771-1
	CDKN2A	ENST00000498124.1	TSL:1	c.146T>C	p.Ile49Thr	missense	Exon 1 of 4	ENSP00000418915.1	P42771-4
	CDKN2A	ENST00000579755.2	TSL:1 MANE Plus Clinical	c.194-3474T>C		intron	N/A	ENSP00000462950.1	Q8N726-1

Frequencies

GnomAD3 genomes AF: 0.0000723 AC: 11 AN: 152096 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000655

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: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000625 AC: 156 AN: 249454 AF XY: 0.000489

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00451

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000114 AC: 167 AN: 1461744 Hom.: 0 Cov.: 32 AF XY: 0.000102 AC XY: 74 AN XY: 727178

African (AFR) AF: 0.00 AC: 0 AN: 33478

American (AMR) AF: 0.00369 AC: 165 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26132

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53286

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

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1112004

Other (OTH) AF: 0.0000331 AC: 2 AN: 60394

GnomAD4 genome AF: 0.0000723 AC: 11 AN: 152212 Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9 AN XY: 74428

African (AFR) AF: 0.0000241 AC: 1 AN: 41536

American (AMR) AF: 0.000654 AC: 10 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5154

South Asian (SAS) AF: 0.00 AC: 0 AN: 4812

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10614

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68016

Other (OTH) AF: 0.00 AC: 0 AN: 2112

Alfa AF: 0.000120 Hom.: 1

Bravo AF: 0.000298

ExAC AF: 0.000436 AC: 53

ClinVar

ClinVar submissions

Significance: Conflicting classifications of pathogenicity

Revision: criteria provided, conflicting classifications

Pathogenic	VUS	Benign	Condition
2	2	-	Hereditary cancer-predisposing syndrome (4)
2	-	-	CDKN2A-related disorder (2)
1	1	-	Melanoma-pancreatic cancer syndrome (2)
-	2	-	not provided (2)
-	2	-	not specified (2)
-	1	-	Acute lymphoid leukemia (1)
1	-	-	Familial melanoma (1)
-	1	-	Melanoma and neural system tumor syndrome (1)
1	-	-	Melanoma and neural system tumor syndrome;C1835044:Melanoma, cutaneous malignant, susceptibility to, 2;C1838547:Melanoma-pancreatic cancer syndrome (1)
-	1	-	Osteoblastic osteosarcoma (1)
-	-	-	Melanoma and neural system tumor syndrome;C1838547:Melanoma-pancreatic cancer syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Uncertain	0.070
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.47	T
Eigen	Uncertain	0.51
Eigen_PC	Uncertain	0.46
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.93	D
M_CAP	Pathogenic	0.58	D
MetaRNN	Benign	0.063	T
MetaSVM	Uncertain	0.0011	D
PhyloP100		5.6
PrimateAI	Pathogenic	0.80	T
PROVEAN	Uncertain	-3.8	D
REVEL	Uncertain	0.60
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.0030	D
Polyphen		1.0	D
Vest4		0.70
MVP		0.99
MPC		1.4
ClinPred		0.25	T
GERP RS		4.9
PromoterAI		-0.033	Neutral
Varity_R		0.49
gMVP		0.98
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: rs199907548; hg19: chr9-21974681; COSMIC: COSV58687879;