9-21967856-G-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000077.5(CDKN2A):c.*373C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00909 in 336,948 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.016 ( 56 hom., cov: 33)
Exomes 𝑓: 0.0034 ( 11 hom. )
Consequence
CDKN2A
NM_000077.5 3_prime_UTR
NM_000077.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.165
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 9-21967856-G-C is Benign according to our data. Variant chr9-21967856-G-C is described in ClinVar as [Benign]. Clinvar id is 1181894.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0507 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDKN2A | NM_000077.5 | c.*373C>G | 3_prime_UTR_variant | 3/3 | ENST00000304494.10 | NP_000068.1 | ||
CDKN2A | NM_058195.4 | c.*488C>G | 3_prime_UTR_variant | 3/3 | ENST00000579755.2 | NP_478102.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDKN2A | ENST00000304494.10 | c.*373C>G | 3_prime_UTR_variant | 3/3 | 1 | NM_000077.5 | ENSP00000307101 | P2 | ||
CDKN2A | ENST00000579755.2 | c.*488C>G | 3_prime_UTR_variant | 3/3 | 1 | NM_058195.4 | ENSP00000462950 |
Frequencies
GnomAD3 genomes AF: 0.0160 AC: 2428AN: 152200Hom.: 55 Cov.: 33
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GnomAD4 exome AF: 0.00337 AC: 622AN: 184628Hom.: 11 Cov.: 0 AF XY: 0.00311 AC XY: 289AN XY: 92780
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GnomAD4 genome AF: 0.0160 AC: 2440AN: 152320Hom.: 56 Cov.: 33 AF XY: 0.0153 AC XY: 1141AN XY: 74490
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at