rs9479
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000268059.10(PML):c.*284A>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 0.501 in 1,526,804 control chromosomes in the GnomAD database, including 192,950 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.51 ( 19502 hom., cov: 31)
Exomes 𝑓: 0.50 ( 173448 hom. )
Consequence
PML
ENST00000268059.10 3_prime_UTR
ENST00000268059.10 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.515
Genes affected
PML (HGNC:9113): (PML nuclear body scaffold) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 15-74036235-A-G is Benign according to our data. Variant chr15-74036235-A-G is described in ClinVar as [Benign]. Clinvar id is 1288742.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PML | NM_033238.3 | c.1710+1705A>G | intron_variant | ENST00000268058.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PML | ENST00000268058.8 | c.1710+1705A>G | intron_variant | 1 | NM_033238.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.505 AC: 76655AN: 151700Hom.: 19493 Cov.: 31
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GnomAD4 exome AF: 0.501 AC: 688672AN: 1374986Hom.: 173448 Cov.: 51 AF XY: 0.502 AC XY: 340204AN XY: 677800
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GnomAD4 genome ? AF: 0.505 AC: 76715AN: 151818Hom.: 19502 Cov.: 31 AF XY: 0.509 AC XY: 37749AN XY: 74188
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2020 | This variant is associated with the following publications: (PMID: 24886876) - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at