Variant chr7-16215977-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001101426.4(CRPPA):c.1251+89T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 1,037,554 control chromosomes in the GnomAD database, including 224,018 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.64 ( 31397 hom., cov: 32)

Exomes 𝑓: 0.66 ( 192621 hom. )

Consequence

CRPPA
NM_001101426.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.501

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 7-16215977-A-T is Benign according to our data. Variant chr7-16215977-A-T is described in ClinVar as [Benign]. Clinvar id is 682001.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRPPA	NM_001101426.4 linkuse as main transcript	c.1251+89T>A		intron_variant		ENST00000407010.7
CRPPA-AS1	NR_038947.1 linkuse as main transcript	n.118+5374A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRPPA	ENST00000407010.7 linkuse as main transcript	c.1251+89T>A		intron_variant		5	NM_001101426.4	P1	A4D126-1
CRPPA-AS1	ENST00000438573.5 linkuse as main transcript	n.116+5374A>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.640

AC:

97265

AN:

151942

Hom.:

31358

Cov.:

show subpopulations

Gnomad AFR

AF:

0.557

Gnomad AMI

AF:

0.623

Gnomad AMR

AF:

0.694

Gnomad ASJ

AF:

0.625

Gnomad EAS

AF:

0.507

Gnomad SAS

AF:

0.651

Gnomad FIN

AF:

0.738

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.674

Gnomad OTH

AF:

0.628

GnomAD4 exome

AF:

0.657

AC:

581967

AN:

885494

Hom.:

192621

AF XY:

0.657

AC XY:

295872

AN XY:

450526

show subpopulations

Gnomad4 AFR exome

AF:

0.546

Gnomad4 AMR exome

AF:

0.710

Gnomad4 ASJ exome

AF:

0.616

Gnomad4 EAS exome

AF:

0.481

Gnomad4 SAS exome

AF:

0.641

Gnomad4 FIN exome

AF:

0.732

Gnomad4 NFE exome

AF:

0.665

Gnomad4 OTH exome

AF:

0.651

GnomAD4 genome

AF:

0.640

AC:

97355

AN:

152060

Hom.:

31397

Cov.:

AF XY:

0.645

AC XY:

47965

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.558

Gnomad4 AMR

AF:

0.694

Gnomad4 ASJ

AF:

0.625

Gnomad4 EAS

AF:

0.506

Gnomad4 SAS

AF:

0.652

Gnomad4 FIN

AF:

0.738

Gnomad4 NFE

AF:

0.674

Gnomad4 OTH

AF:

0.628

Alfa

AF:

0.564

Hom.:

1690

Bravo

AF:

0.630

Asia WGS

AF:

0.617

AC:

2134

AN:

3462

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 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

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.2

DANN

Benign

0.69

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