1-156240066-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001199662.1(PMF1-BGLAP):c.565-2487C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 157,184 control chromosomes in the GnomAD database, including 4,059 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.22 ( 3953 hom., cov: 32)
Exomes 𝑓: 0.19 ( 106 hom. )
Consequence
PMF1-BGLAP
NM_001199662.1 intron
NM_001199662.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.116
Genes affected
PMF1 (HGNC:9112): (polyamine modulated factor 1) Enables leucine zipper domain binding activity and transcription coactivator activity. Involved in chromosome segregation. Located in Golgi apparatus; kinetochore; and nucleoplasm. Part of MIS12/MIND type complex. Implicated in bladder carcinoma and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PMF1-BGLAP | NM_001199662.1 | c.565-2487C>T | intron_variant | ||||
PMF1 | NM_007221.4 | downstream_gene_variant | ENST00000368277.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PMF1 | ENST00000368277.3 | downstream_gene_variant | 1 | NM_007221.4 | P1 | ||||
PMF1 | ENST00000368279.7 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.221 AC: 33585AN: 152054Hom.: 3936 Cov.: 32
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GnomAD4 exome AF: 0.187 AC: 935AN: 5012Hom.: 106 Cov.: 0 AF XY: 0.191 AC XY: 529AN XY: 2770
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GnomAD4 genome ? AF: 0.221 AC: 33636AN: 152172Hom.: 3953 Cov.: 32 AF XY: 0.220 AC XY: 16394AN XY: 74386
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ClinVar
Not reported inComputational scores
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Name
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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