chr7-16091661-G-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_StrongBS1

The NM_001101426.4(CRPPA):​c.*34C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000267 in 1,190,706 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: 𝑓 0.0014 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 0 hom. )

Consequence

CRPPA
NM_001101426.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0900
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 Likely_benign. Variant got -6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00135 (206/152196) while in subpopulation AFR AF= 0.00486 (202/41538). AF 95% confidence interval is 0.00431. There are 0 homozygotes in gnomad4. There are 91 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CRPPANM_001101426.4 linkc.*34C>T 3_prime_UTR_variant Exon 10 of 10 ENST00000407010.7 NP_001094896.1 A4D126-1
CRPPANM_001368197.1 linkc.*34C>T 3_prime_UTR_variant Exon 9 of 9 NP_001355126.1
CRPPANM_001101417.4 linkc.*34C>T 3_prime_UTR_variant Exon 9 of 9 NP_001094887.1 A4D126-2A0A140VJM1
CRPPANR_160656.1 linkn.1455C>T non_coding_transcript_exon_variant Exon 8 of 8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CRPPAENST00000407010 linkc.*34C>T 3_prime_UTR_variant Exon 10 of 10 5 NM_001101426.4 ENSP00000385478.2 A4D126-1
CRPPAENST00000399310 linkc.*34C>T 3_prime_UTR_variant Exon 9 of 9 1 ENSP00000382249.3 A4D126-2
CRPPAENST00000676325 linkc.*34C>T 3_prime_UTR_variant Exon 11 of 11 ENSP00000502074.1 A0A6Q8PG39
CRPPAENST00000675257 linkc.*34C>T 3_prime_UTR_variant Exon 10 of 10 ENSP00000501664.1 A0A6Q8PF75

Frequencies

GnomAD3 genomes
AF:
0.00135
AC:
205
AN:
152078
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00485
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000197
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000339
AC:
50
AN:
147588
Hom.:
0
AF XY:
0.000296
AC XY:
23
AN XY:
77756
show subpopulations
Gnomad AFR exome
AF:
0.00535
Gnomad AMR exome
AF:
0.000369
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000974
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000108
AC:
112
AN:
1038510
Hom.:
0
Cov.:
13
AF XY:
0.000102
AC XY:
54
AN XY:
527722
show subpopulations
Gnomad4 AFR exome
AF:
0.00384
Gnomad4 AMR exome
AF:
0.000274
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000296
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.000216
GnomAD4 genome
AF:
0.00135
AC:
206
AN:
152196
Hom.:
0
Cov.:
33
AF XY:
0.00122
AC XY:
91
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.00486
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000113
Hom.:
41
Bravo
AF:
0.00155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.4
DANN
Benign
0.57

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: rs16878689; hg19: chr7-16131286; API