chr7-16088411-T-C
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001101426.4(CRPPA):c.*3284A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000092 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CRPPA
NM_001101426.4 3_prime_UTR
NM_001101426.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.32
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 Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 7-16088411-T-C is Benign according to our data. Variant chr7-16088411-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 908678.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRPPA | NM_001101426.4 | c.*3284A>G | 3_prime_UTR_variant | 10/10 | ENST00000407010.7 | ||
CRPPA | NM_001101417.4 | c.*3284A>G | 3_prime_UTR_variant | 9/9 | |||
CRPPA | NM_001368197.1 | c.*3284A>G | 3_prime_UTR_variant | 9/9 | |||
CRPPA | NR_160656.1 | n.4705A>G | non_coding_transcript_exon_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRPPA | ENST00000407010.7 | c.*3284A>G | 3_prime_UTR_variant | 10/10 | 5 | NM_001101426.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000925 AC: 10AN: 108160Hom.: 0 Cov.: 30
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 44Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 32
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000925 AC: 10AN: 108160Hom.: 0 Cov.: 30 AF XY: 0.000158 AC XY: 8AN XY: 50776
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital Muscular Dystrophy, alpha-dystroglycan related Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
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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