chr7-16088412-C-CTT
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001101426.4(CRPPA):c.*3282_*3283insAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.21 ( 3161 hom., cov: 0)
Failed GnomAD Quality Control
Consequence
CRPPA
NM_001101426.4 3_prime_UTR
NM_001101426.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.953
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 -8 ACMG points.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRPPA | NM_001101426.4 | c.*3282_*3283insAA | 3_prime_UTR_variant | 10/10 | ENST00000407010.7 | ||
CRPPA | NM_001101417.4 | c.*3282_*3283insAA | 3_prime_UTR_variant | 9/9 | |||
CRPPA | NM_001368197.1 | c.*3282_*3283insAA | 3_prime_UTR_variant | 9/9 | |||
CRPPA | NR_160656.1 | n.4703_4704insAA | non_coding_transcript_exon_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRPPA | ENST00000407010.7 | c.*3282_*3283insAA | 3_prime_UTR_variant | 10/10 | 5 | NM_001101426.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.215 AC: 23735AN: 110462Hom.: 3162 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
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Data not reliable, filtered out with message: AC0
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GnomAD4 genome AF: 0.215 AC: 23722AN: 110468Hom.: 3161 Cov.: 0 AF XY: 0.202 AC XY: 10343AN XY: 51166
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Congenital Muscular Dystrophy, alpha-dystroglycan related Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at