rs17279573
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000502774.1(WDR45P1):n.565A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.149 in 1,598,682 control chromosomes in the GnomAD database, including 19,603 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 0.11 ( 1281 hom., cov: 33)
Exomes 𝑓: 0.15 ( 18322 hom. )
Consequence
WDR45P1
ENST00000502774.1 non_coding_transcript_exon
ENST00000502774.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.95
Genes affected
WDR45P1 (HGNC:52406): (WD repeat domain 45 pseudogene 1)
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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=-0.57).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC100419170 | NR_134873.1 | n.355+18119A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR45P1 | ENST00000502774.1 | n.565A>G | non_coding_transcript_exon_variant | 1/1 | |||||
ENST00000602666.1 | n.355+18119A>G | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.114 AC: 17388AN: 152040Hom.: 1282 Cov.: 33
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GnomAD4 exome AF: 0.153 AC: 221323AN: 1446524Hom.: 18322 Cov.: 36 AF XY: 0.154 AC XY: 110958AN XY: 720288
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GnomAD4 genome ? AF: 0.114 AC: 17382AN: 152158Hom.: 1281 Cov.: 33 AF XY: 0.114 AC XY: 8455AN 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