GeneBe

7-16258956-G-T

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001101426.4(CRPPA):​c.990C>A​(p.Ile330Ile) 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 1,459,050 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

CRPPA
NM_001101426.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.88

Publications

0 publications found
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]
CRPPA-AS1 (HGNC:48962): (CRPPA antisense RNA 1)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001101426.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CRPPA
NM_001101426.4
MANE Select
c.990C>Ap.Ile330Ile
synonymous
Exon 7 of 10NP_001094896.1
CRPPA
NM_001368197.1
c.885C>Ap.Ile295Ile
synonymous
Exon 6 of 9NP_001355126.1
CRPPA
NM_001101417.4
c.840C>Ap.Ile280Ile
synonymous
Exon 6 of 9NP_001094887.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CRPPA
ENST00000407010.7
TSL:5 MANE Select
c.990C>Ap.Ile330Ile
synonymous
Exon 7 of 10ENSP00000385478.2
CRPPA
ENST00000399310.3
TSL:1
c.840C>Ap.Ile280Ile
synonymous
Exon 6 of 9ENSP00000382249.3
CRPPA-AS1
ENST00000438573.5
TSL:1
n.222-2943G>T
intron
N/A

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1459050
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
725724
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33378
American (AMR)
AF:
0.00
AC:
0
AN:
44392
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26056
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39610
South Asian (SAS)
AF:
0.00
AC:
0
AN:
85912
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53266
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
9.01e-7
AC:
1
AN:
1110450
Other (OTH)
AF:
0.00
AC:
0
AN:
60230
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
6.1
DANN
Benign
0.80
PhyloP100
1.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.32
Details are displayed if max score is > 0.2
DS_DL_spliceai
0.32
Position offset: -36

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

Publications

Other links and lift over

dbSNP: rs373422736; hg19: chr7-16298581; COSMIC: COSV67906065; API