rs7258489
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_172902.1(PPP5D1P):n.34+999G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,166 control chromosomes in the GnomAD database, including 6,138 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 0.28 ( 6137 hom., cov: 32)
Exomes 𝑓: 0.35 ( 1 hom. )
Consequence
PPP5D1P
NR_172902.1 intron, non_coding_transcript
NR_172902.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.14
Genes affected
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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=-0.98).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP5D1P | NR_172902.1 | n.34+999G>A | intron_variant, non_coding_transcript_variant | ||||
PPP5D1P | NR_172903.1 | n.34+999G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP5D1P | ENST00000602017.7 | n.107+999G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.282 AC: 42940AN: 152022Hom.: 6145 Cov.: 32
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GnomAD4 exome AF: 0.346 AC: 9AN: 26Hom.: 1 Cov.: 0 AF XY: 0.438 AC XY: 7AN XY: 16
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GnomAD4 genome ? AF: 0.282 AC: 42953AN: 152140Hom.: 6137 Cov.: 32 AF XY: 0.283 AC XY: 21019AN XY: 74374
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ClinVar
Not reported inComputational scores
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Name
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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