chr17-38735214-T-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_007144.3(PCGF2):c.*9A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000738 in 1,396,522 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000060 ( 0 hom. )
Consequence
PCGF2
NM_007144.3 3_prime_UTR
NM_007144.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0330
Genes affected
CISD3 (HGNC:27578): (CDGSH iron sulfur domain 3) CISD3 is a member of the CDGSH domain-containing family, which may play a role in regulating electron transport and oxidative phosphorylation (Wiley et al., 2007 [PubMed 17376863]).[supplied by OMIM, Apr 2008]
PCGF2 (HGNC:12929): (polycomb group ring finger 2) The protein encoded by this gene contains a RING finger motif and is similar to the polycomb group (PcG) gene products. PcG gene products form complexes via protein-protein interaction and maintain the transcription repression of genes involved in embryogenesis, cell cycles, and tumorigenesis. This protein was shown to act as a negative regulator of transcription and has tumor suppressor activity. The expression of this gene was detected in various tumor cells, but is limited in neural organs in normal tissues. Knockout studies in mice suggested that this protein may negatively regulate the expression of different cytokines, chemokines, and chemokine receptors, and thus plays an important role in lymphocyte differentiation and migration, as well as in immune responses. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 17-38735214-T-A is Benign according to our data. Variant chr17-38735214-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 3048124.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 28 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CISD3 | NM_001136498.2 | c.*1759T>A | 3_prime_UTR_variant | 4/4 | ENST00000613478.2 | ||
PCGF2 | NM_007144.3 | c.*9A>T | 3_prime_UTR_variant | 11/11 | ENST00000620225.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CISD3 | ENST00000613478.2 | c.*1759T>A | 3_prime_UTR_variant | 4/4 | 2 | NM_001136498.2 | P1 | ||
PCGF2 | ENST00000620225.5 | c.*9A>T | 3_prime_UTR_variant | 11/11 | 1 | NM_007144.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000185 AC: 28AN: 150962Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000638 AC: 43AN: 67418Hom.: 0 AF XY: 0.000422 AC XY: 14AN XY: 33200
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GnomAD4 exome AF: 0.0000602 AC: 75AN: 1245446Hom.: 0 Cov.: 33 AF XY: 0.0000433 AC XY: 26AN XY: 600888
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GnomAD4 genome ? AF: 0.000185 AC: 28AN: 151076Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 73782
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PCGF2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 23, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at