Variant rs139478143 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001101426.4(CRPPA):c.1026+45_1026+46del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 1,194,472 control chromosomes in the GnomAD database, including 10,114 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.091 ( 798 hom., cov: 31)

Exomes 𝑓: 0.13 ( 9316 hom. )

Consequence

CRPPA
NM_001101426.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.34

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 links:

CRPPA-AS1 (HGNC:48962): (CRPPA antisense RNA 1)

CRPPA-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 7-16258873-CAT-C is Benign according to our data. Variant chr7-16258873-CAT-C is described in ClinVar as [Benign]. Clinvar id is 257461.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRPPA	NM_001101426.4 linkuse as main transcript	c.1026+45_1026+46del		intron_variant		ENST00000407010.7	NP_001094896.1
CRPPA-AS1	NR_038947.1 linkuse as main transcript	n.241-7353_241-7352del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRPPA	ENST00000407010.7 linkuse as main transcript	c.1026+45_1026+46del		intron_variant		5	NM_001101426.4	ENSP00000385478	P1	A4D126-1
CRPPA-AS1	ENST00000438573.5 linkuse as main transcript	n.222-3025_222-3024del		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0908

AC:

13803

AN:

151968

Hom.:

798

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0256

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.0726

Gnomad ASJ

AF:

0.0712

Gnomad EAS

AF:

0.141

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.0955

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.108

GnomAD3 exomes

AF:

0.112

AC:

20027

AN:

179064

Hom.:

1336

AF XY:

0.120

AC XY:

11518

AN XY:

96382

show subpopulations

Gnomad AFR exome

AF:

0.0224

Gnomad AMR exome

AF:

0.0461

Gnomad ASJ exome

AF:

0.0733

Gnomad EAS exome

AF:

0.146

Gnomad SAS exome

AF:

0.166

Gnomad FIN exome

AF:

0.0955

Gnomad NFE exome

AF:

0.131

Gnomad OTH exome

AF:

0.112

GnomAD4 exome

AF:

0.128

AC:

133735

AN:

1042386

Hom.:

9316

AF XY:

0.130

AC XY:

69187

AN XY:

531696

show subpopulations

Gnomad4 AFR exome

AF:

0.0229

Gnomad4 AMR exome

AF:

0.0494

Gnomad4 ASJ exome

AF:

0.0695

Gnomad4 EAS exome

AF:

0.129

Gnomad4 SAS exome

AF:

0.170

Gnomad4 FIN exome

AF:

0.0983

Gnomad4 NFE exome

AF:

0.135

Gnomad4 OTH exome

AF:

0.123

GnomAD4 genome

AF:

0.0907

AC:

13794

AN:

152086

Hom.:

798

Cov.:

AF XY:

0.0903

AC XY:

6714

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0255

Gnomad4 AMR

AF:

0.0724

Gnomad4 ASJ

AF:

0.0712

Gnomad4 EAS

AF:

0.141

Gnomad4 SAS

AF:

0.146

Gnomad4 FIN

AF:

0.0955

Gnomad4 NFE

AF:

0.126

Gnomad4 OTH

AF:

0.108

Alfa

AF:

0.102

Hom.:

172

Bravo

AF:

0.0863

Asia WGS

AF:

0.109

AC:

376

AN:

3470

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over