rs11580218
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000487348.1(PPIAP34):n.338C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0293 in 1,049,902 control chromosomes in the GnomAD database, including 614 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 0.024 ( 66 hom., cov: 32)
Exomes 𝑓: 0.030 ( 548 hom. )
Consequence
PPIAP34
ENST00000487348.1 non_coding_transcript_exon
ENST00000487348.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.575
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=-0.58).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0241 (3660/152126) while in subpopulation NFE AF= 0.0383 (2606/68004). AF 95% confidence interval is 0.0371. There are 66 homozygotes in gnomad4. There are 1651 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 66 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPIAP34 | ENST00000487348.1 | n.338C>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0241 AC: 3662AN: 152008Hom.: 66 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.0302 AC: 27096AN: 897776Hom.: 548 Cov.: 13 AF XY: 0.0299 AC XY: 14037AN XY: 469564
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GnomAD4 genome ? AF: 0.0241 AC: 3660AN: 152126Hom.: 66 Cov.: 32 AF XY: 0.0222 AC XY: 1651AN XY: 74378
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at