chr13-72792566-A-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006346.4(PIBF1):c.353+19A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 1,074,314 control chromosomes in the GnomAD database, including 56,465 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.31 ( 7989 hom., cov: 30)
Exomes 𝑓: 0.33 ( 48476 hom. )
Consequence
PIBF1
NM_006346.4 intron
NM_006346.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.581
Genes affected
PIBF1 (HGNC:23352): (progesterone immunomodulatory binding factor 1) This gene encodes a protein that is induced by the steroid hormone progesterone and plays a role in the maintenance of pregnancy. The encoded protein regulates multiple facets of the immune system to promote normal pregnancy including cytokine synthesis, natural killer (NK) cell activity, and arachidonic acid metabolism. Low serum levels of this protein have been associated with spontaneous pre-term labor in humans. This protein may promote the proliferation, migration and invasion of glioma. [provided by RefSeq, Mar 2017]
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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=-0.86).
BP6
Variant 13-72792566-A-T is Benign according to our data. Variant chr13-72792566-A-T is described in ClinVar as [Benign]. Clinvar id is 1530576.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIBF1 | NM_006346.4 | c.353+19A>T | intron_variant | ENST00000326291.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIBF1 | ENST00000326291.11 | c.353+19A>T | intron_variant | 1 | NM_006346.4 | P1 | |||
PIBF1 | ENST00000615625.1 | c.-262+10217A>T | intron_variant | 1 | |||||
PIBF1 | ENST00000617689.4 | c.353+19A>T | intron_variant | 1 | |||||
PIBF1 | ENST00000489797.1 | n.297+19A>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.305 AC: 45713AN: 149726Hom.: 7979 Cov.: 30
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GnomAD3 exomes AF: 0.398 AC: 59166AN: 148832Hom.: 10046 AF XY: 0.402 AC XY: 33107AN XY: 82402
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GnomAD4 exome AF: 0.328 AC: 303595AN: 924478Hom.: 48476 Cov.: 13 AF XY: 0.334 AC XY: 158388AN XY: 474544
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GnomAD4 genome AF: 0.305 AC: 45755AN: 149836Hom.: 7989 Cov.: 30 AF XY: 0.314 AC XY: 22962AN XY: 73116
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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 | Invitae | Jan 29, 2024 | - - |
Computational scores
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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