NM_001101426.4:c.1252-10822T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001101426.4(CRPPA):​c.1252-10822T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 151,798 control chromosomes in the GnomAD database, including 48,457 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 0.79 ( 48457 hom., cov: 32)

Consequence

CRPPA
NM_001101426.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.237
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CRPPANM_001101426.4 linkc.1252-10822T>C intron_variant Intron 9 of 9 ENST00000407010.7 NP_001094896.1 A4D126-1
CRPPANM_001368197.1 linkc.1147-10822T>C intron_variant Intron 8 of 8 NP_001355126.1
CRPPANM_001101417.4 linkc.1102-10822T>C intron_variant Intron 8 of 8 NP_001094887.1 A4D126-2A0A140VJM1
CRPPANR_160656.1 linkn.1317-10822T>C intron_variant Intron 7 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CRPPAENST00000407010.7 linkc.1252-10822T>C intron_variant Intron 9 of 9 5 NM_001101426.4 ENSP00000385478.2 A4D126-1
CRPPAENST00000399310.3 linkc.1102-10822T>C intron_variant Intron 8 of 8 1 ENSP00000382249.3 A4D126-2
CRPPAENST00000676325.1 linkc.949-10822T>C intron_variant Intron 10 of 10 ENSP00000502074.1 A0A6Q8PG39
CRPPAENST00000675257.1 linkc.844-10822T>C intron_variant Intron 9 of 9 ENSP00000501664.1 A0A6Q8PF75

Frequencies

GnomAD3 genomes
AF:
0.788
AC:
119461
AN:
151680
Hom.:
48429
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.577
Gnomad AMI
AF:
0.856
Gnomad AMR
AF:
0.884
Gnomad ASJ
AF:
0.924
Gnomad EAS
AF:
0.822
Gnomad SAS
AF:
0.857
Gnomad FIN
AF:
0.885
Gnomad MID
AF:
0.829
Gnomad NFE
AF:
0.863
Gnomad OTH
AF:
0.811
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.787
AC:
119532
AN:
151798
Hom.:
48457
Cov.:
32
AF XY:
0.792
AC XY:
58752
AN XY:
74174
show subpopulations
Gnomad4 AFR
AF:
0.577
Gnomad4 AMR
AF:
0.884
Gnomad4 ASJ
AF:
0.924
Gnomad4 EAS
AF:
0.821
Gnomad4 SAS
AF:
0.857
Gnomad4 FIN
AF:
0.885
Gnomad4 NFE
AF:
0.863
Gnomad4 OTH
AF:
0.813
Alfa
AF:
0.787
Hom.:
2647
Bravo
AF:
0.779
Asia WGS
AF:
0.845
AC:
2938
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
2.7
DANN
Benign
0.41

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7798339; hg19: chr7-16142246; API