rs541412708
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001101426.4(CRPPA):āc.408A>Gā(p.Ala136=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000656 in 152,372 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 (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 33)
Consequence
CRPPA
NM_001101426.4 synonymous
NM_001101426.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.42
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 -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 7-16406187-T-C is Benign according to our data. Variant chr7-16406187-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 540373.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.42 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRPPA | NM_001101426.4 | c.408A>G | p.Ala136= | synonymous_variant | 2/10 | ENST00000407010.7 | |
CRPPA | NM_001368197.1 | c.408A>G | p.Ala136= | synonymous_variant | 2/9 | ||
CRPPA | NM_001101417.4 | c.408A>G | p.Ala136= | synonymous_variant | 2/9 | ||
CRPPA | NR_160656.1 | n.624A>G | non_coding_transcript_exon_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRPPA | ENST00000407010.7 | c.408A>G | p.Ala136= | synonymous_variant | 2/10 | 5 | NM_001101426.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152254Hom.: 0 Cov.: 33
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GnomAD4 exome Cov.: 33
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GnomAD4 genome ? AF: 0.00000656 AC: 1AN: 152372Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74508
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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 | Invitae | Dec 18, 2017 | - - |
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