rs883534
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_018699.4(PRDM5):c.177+9089A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 152,356 control chromosomes in the GnomAD database, including 25 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 0.012 ( 25 hom., cov: 32)
Consequence
PRDM5
NM_018699.4 intron
NM_018699.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.23
Genes affected
PRDM5 (HGNC:9349): (PR/SET domain 5) The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. [provided by RefSeq, Jul 2008]
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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=-0.9).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0124 (1887/152356) while in subpopulation SAS AF= 0.0307 (148/4826). AF 95% confidence interval is 0.0266. There are 25 homozygotes in gnomad4. There are 916 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 25 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM5 | NM_018699.4 | c.177+9089A>G | intron_variant | ENST00000264808.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM5 | ENST00000264808.8 | c.177+9089A>G | intron_variant | 1 | NM_018699.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0124 AC: 1887AN: 152238Hom.: 25 Cov.: 32
GnomAD3 genomes
?
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1887
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0124 AC: 1887AN: 152356Hom.: 25 Cov.: 32 AF XY: 0.0123 AC XY: 916AN XY: 74504
GnomAD4 genome
?
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AC:
1887
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152356
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32
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916
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74504
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40
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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