rs2292399
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000303202.8(PPDPFL):c.*140A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 1,506,684 control chromosomes in the GnomAD database, including 102,531 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 0.31 ( 8228 hom., cov: 32)
Exomes 𝑓: 0.37 ( 94303 hom. )
Consequence
PPDPFL
ENST00000303202.8 3_prime_UTR
ENST00000303202.8 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.644
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=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPDPFL | NM_001256597.2 | c.233+338A>G | intron_variant | ENST00000522267.6 | |||
PPDPFL | NM_001256598.2 | c.*140A>G | 3_prime_UTR_variant | 5/5 | |||
PPDPFL | NM_001007176.5 | c.233+338A>G | intron_variant | ||||
PPDPFL | NM_001256596.1 | c.233+338A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPDPFL | ENST00000303202.8 | c.*140A>G | 3_prime_UTR_variant | 5/5 | 1 | ||||
PPDPFL | ENST00000522267.6 | c.233+338A>G | intron_variant | 2 | NM_001256597.2 | ||||
PPDPFL | ENST00000399653.8 | c.233+338A>G | intron_variant | 1 | P1 | ||||
PPDPFL | ENST00000517663.5 | c.233+338A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.313 AC: 47542AN: 151962Hom.: 8227 Cov.: 32
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GnomAD4 exome AF: 0.368 AC: 497921AN: 1354606Hom.: 94303 Cov.: 33 AF XY: 0.363 AC XY: 241524AN XY: 665198
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GnomAD4 genome ? AF: 0.313 AC: 47558AN: 152078Hom.: 8228 Cov.: 32 AF XY: 0.314 AC XY: 23358AN XY: 74328
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at