rs876537
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The ENST00000412857.1(CRPP1):n.465G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.358 in 241,664 control chromosomes in the GnomAD database, including 16,438 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 0.35 ( 9827 hom., cov: 32)
Exomes 𝑓: 0.38 ( 6611 hom. )
Consequence
CRPP1
ENST00000412857.1 non_coding_transcript_exon
ENST00000412857.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.01
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.24).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRPP1 | ENST00000412857.1 | n.465G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.346 AC: 52643AN: 152016Hom.: 9822 Cov.: 32
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GnomAD4 exome AF: 0.379 AC: 33908AN: 89530Hom.: 6611 Cov.: 0 AF XY: 0.378 AC XY: 19644AN XY: 52024
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GnomAD4 genome AF: 0.346 AC: 52664AN: 152134Hom.: 9827 Cov.: 32 AF XY: 0.348 AC XY: 25898AN XY: 74374
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at