rs754348253
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001101426.4(CRPPA):c.816G>T(p.Ala272=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,534 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
CRPPA
NM_001101426.4 synonymous
NM_001101426.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.19
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 -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
Variant 7-16301440-C-A is Benign according to our data. Variant chr7-16301440-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1680766.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.19 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRPPA | NM_001101426.4 | c.816G>T | p.Ala272= | synonymous_variant | 5/10 | ENST00000407010.7 | NP_001094896.1 | |
CRPPA | NM_001368197.1 | c.711G>T | p.Ala237= | synonymous_variant | 4/9 | NP_001355126.1 | ||
CRPPA | NM_001101417.4 | c.666G>T | p.Ala222= | synonymous_variant | 4/9 | NP_001094887.1 | ||
CRPPA | NR_160656.1 | n.901-23214G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRPPA | ENST00000407010.7 | c.816G>T | p.Ala272= | synonymous_variant | 5/10 | 5 | NM_001101426.4 | ENSP00000385478 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248094Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134518
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GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460534Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 726488
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7;C5190987:Autosomal recessive limb-girdle muscular dystrophy type 2U Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 31, 2023 | - - |
Computational scores
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Name
Calibrated prediction
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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