rs2389591
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001101426.4(CRPPA):c.1251+26249T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,060 control chromosomes in the GnomAD database, including 39,703 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 0.72 ( 39703 hom., cov: 32)
Consequence
CRPPA
NM_001101426.4 intron
NM_001101426.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.782
Genes affected
CRPPA (HGNC:37276): (CDP-L-ribitol pyrophosphorylase A) This gene encodes a 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase-like protein. Mutations in this gene are the cause of Walker-Warburg syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2012]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRPPA | NM_001101426.4 | c.1251+26249T>C | intron_variant | ENST00000407010.7 | |||
CRPPA | NM_001101417.4 | c.1101+26249T>C | intron_variant | ||||
CRPPA | NM_001368197.1 | c.1146+26249T>C | intron_variant | ||||
CRPPA | NR_160656.1 | n.1316+26249T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRPPA | ENST00000407010.7 | c.1251+26249T>C | intron_variant | 5 | NM_001101426.4 | P1 | |||
CRPPA | ENST00000399310.3 | c.1101+26249T>C | intron_variant | 1 | |||||
CRPPA | ENST00000675257.1 | c.843+26249T>C | intron_variant | ||||||
CRPPA | ENST00000676325.1 | c.948+26249T>C | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.719 AC: 109207AN: 151942Hom.: 39655 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.719 AC: 109308AN: 152060Hom.: 39703 Cov.: 32 AF XY: 0.723 AC XY: 53754AN XY: 74318
GnomAD4 genome
?
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32
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53754
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74318
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2748
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3474
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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