rs2725379
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000339382.3(PURG):c.864+10370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.975 in 152,280 control chromosomes in the GnomAD database, including 72,505 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 0.98 ( 72505 hom., cov: 32)
Consequence
PURG
ENST00000339382.3 intron
ENST00000339382.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.17
Genes affected
PURG (HGNC:17930): (purine rich element binding protein G) The exact function of this gene is not known, however, its encoded product is highly similar to purine-rich element binding protein A. The latter is a DNA-binding protein which binds preferentially to the single strand of the purine-rich element termed PUR, and has been implicated in the control of both DNA replication and transcription. This gene lies in close proximity to the Werner syndrome gene, but on the opposite strand, on chromosome 8p11. [provided by RefSeq, Apr 2016]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PURG | NM_001015508.3 | c.864+10370G>A | intron_variant | ||||
PURG | NM_001323312.2 | c.864+10370G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PURG | ENST00000339382.3 | c.864+10370G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.975 AC: 148363AN: 152162Hom.: 72451 Cov.: 32
GnomAD3 genomes
?
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148363
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152162
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32
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GnomAD4 genome ? AF: 0.975 AC: 148476AN: 152280Hom.: 72505 Cov.: 32 AF XY: 0.976 AC XY: 72665AN XY: 74460
GnomAD4 genome
?
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148476
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32
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72665
AN XY:
74460
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Asia WGS
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3461
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at