chr7-16308637-A-AAAC

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001101426.4(CRPPA):c.685-13_685-11dupGTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0263 in 1,406,232 control chromosomes in the GnomAD database, including 1,186 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.045 ( 237 hom., cov: 32)

Exomes 𝑓: 0.024 ( 949 hom. )

Consequence

CRPPA
NM_001101426.4 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 0.808

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 7-16308637-A-AAAC is Benign according to our data. Variant chr7-16308637-A-AAAC is described in ClinVar as [Likely_benign]. Clinvar id is 226676.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CRPPA	NM_001101426.4 link	c.685-13_685-11dupGTT	intron_variant	Intron 3 of 9	ENST00000407010.7	NP_001094896.1	A4D126-1
CRPPA	NM_001368197.1 link	c.685-7174_685-7172dupGTT	intron_variant	Intron 3 of 8		NP_001355126.1
CRPPA	NM_001101417.4 link	c.535-13_535-11dupGTT	intron_variant	Intron 2 of 8		NP_001094887.1	A4D126-2A0A140VJM1
CRPPA	NR_160656.1 link	n.901-30414_901-30412dupGTT	intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRPPA	ENST00000407010.7 link	c.685-11_685-10insGTT		intron_variant	Intron 3 of 9	5	NM_001101426.4	ENSP00000385478.2		A4D126-1

Frequencies

GnomAD3 genomes

AF:

0.0448

AC:

6820

AN:

152162

Hom.:

233

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0699

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.0608

Gnomad ASJ

AF:

0.0533

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.0414

Gnomad FIN

AF:

0.0266

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0201

Gnomad OTH

AF:

0.0521

GnomAD2 exomes

AF:

0.0423

AC:

9287

AN:

219382

AF XY:

0.0395

show subpopulations

Gnomad AFR exome

AF:

0.0636

Gnomad AMR exome

AF:

0.0678

Gnomad ASJ exome

AF:

0.0519

Gnomad EAS exome

AF:

0.157

Gnomad FIN exome

AF:

0.0255

Gnomad NFE exome

AF:

0.0179

Gnomad OTH exome

AF:

0.0393

GnomAD4 exome

AF:

0.0241

AC:

30186

AN:

1253954

Hom.:

949

Cov.:

AF XY:

0.0244

AC XY:

15420

AN XY:

633132

show subpopulations

Gnomad4 AFR exome

AF:

0.0559

AC:

1594

AN:

28498

Gnomad4 AMR exome

AF:

0.0660

AC:

2776

AN:

42072

Gnomad4 ASJ exome

AF:

0.0515

AC:

1267

AN:

24606

Gnomad4 EAS exome

AF:

0.179

AC:

6766

AN:

37884

Gnomad4 SAS exome

AF:

0.0329

AC:

2612

AN:

79484

Gnomad4 FIN exome

AF:

0.0249

AC:

1313

AN:

52742

Gnomad4 NFE exome

AF:

0.0130

AC:

12071

AN:

930110

Gnomad4 Remaining exome

AF:

0.0318

AC:

1691

AN:

53138

Heterozygous variant carriers

1411

2821

4232

5642

7053

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

456

912

1368

1824

2280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0449

AC:

6836

AN:

152278

Hom.:

237

Cov.:

AF XY:

0.0462

AC XY:

3443

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0698

AC:

0.069782

AN:

0.069782

Gnomad4 AMR

AF:

0.0606

AC:

0.060612

AN:

0.060612

Gnomad4 ASJ

AF:

0.0533

AC:

0.0533141

AN:

0.0533141

Gnomad4 EAS

AF:

0.155

AC:

0.1555

AN:

0.1555

Gnomad4 SAS

AF:

0.0412

AC:

0.041235

AN:

0.041235

Gnomad4 FIN

AF:

0.0266

AC:

0.0265637

AN:

0.0265637

Gnomad4 NFE

AF:

0.0201

AC:

0.0200941

AN:

0.0200941

Gnomad4 OTH

AF:

0.0582

AC:

0.0581835

AN:

0.0581835

Heterozygous variant carriers

309

618

927

1236

1545

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0160

Hom.:

Bravo

AF:

0.0507

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6

Feb 09, 2016

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Nov 01, 2023

Athena Diagnostics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jun 25, 2015

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

c.685-13_685-11dup in intron 3 of ISPD: This variant is not expected to have cli nical significance because it has been identified in 17.2% (896/5208) of East As ian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinst itute.org; dbSNP rs142647500). -

Clinical Genetics, Academic Medical Center

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Oct 10, 2014

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:2

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Jun 08, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7;C5190987:Autosomal recessive limb-girdle muscular dystrophy type 2U

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Congenital Muscular Dystrophy, alpha-dystroglycan related

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=100/0

polymorphism (auto)

Splicing

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