Genetic Variant NM_001101426.4:c.*3275_*3282delAAAAAAAA (chr7-16088412-CTTTTTTTT-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001101426.4(CRPPA):c.*3275_*3282delAAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.37 ( 7439 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

CRPPA
NM_001101426.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.13

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 Gene-Disease associations (from GenCC):

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
myopathy caused by variation in CRPPA
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
autosomal recessive limb-girdle muscular dystrophy type 2U
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
congenital muscular dystrophy without intellectual disability
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
muscular dystrophy-dystroglycanopathy, type A
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CRPPA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 7-16088412-CTTTTTTTT-C is Benign according to our data. Variant chr7-16088412-CTTTTTTTT-C is described in ClinVar as [Benign]. Clinvar id is 359494.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CRPPA	NM_001101426.4 link	c.3275_3282delAAAAAAAA	3_prime_UTR_variant	Exon 10 of 10	ENST00000407010.7	NP_001094896.1	A4D126-1
CRPPA	NR_160656.1 link	n.4696_4703delAAAAAAAA	non_coding_transcript_exon_variant	Exon 8 of 8
CRPPA	NM_001368197.1 link	c.3275_3282delAAAAAAAA	3_prime_UTR_variant	Exon 9 of 9		NP_001355126.1
CRPPA	NM_001101417.4 link	c.3275_3282delAAAAAAAA	3_prime_UTR_variant	Exon 9 of 9		NP_001094887.1	A4D126-2A0A140VJM1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRPPA	ENST00000407010.7 link	c.3275_3282delAAAAAAAA		3_prime_UTR_variant	Exon 10 of 10	5	NM_001101426.4	ENSP00000385478.2		A4D126-1

Frequencies

GnomAD3 genomes

AF:

0.375

AC:

42444

AN:

113208

Hom.:

7435

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.297

Gnomad AMR

AF:

0.444

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.391

Gnomad SAS

AF:

0.593

Gnomad FIN

AF:

0.566

Gnomad MID

AF:

0.489

Gnomad NFE

AF:

0.438

Gnomad OTH

AF:

0.366

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.375

AC:

42424

AN:

113192

Hom.:

7439

Cov.:

AF XY:

0.384

AC XY:

20170

AN XY:

52580

show subpopulations

African (AFR)

AF:

0.165

AC:

4567

AN:

27660

American (AMR)

AF:

0.445

AC:

4243

AN:

9534

Ashkenazi Jewish (ASJ)

AF:

0.275

AC:

810

AN:

2944

East Asian (EAS)

AF:

0.391

AC:

1436

AN:

3672

South Asian (SAS)

AF:

0.593

AC:

2260

AN:

3810

European-Finnish (FIN)

AF:

0.566

AC:

2576

AN:

4548

Middle Eastern (MID)

AF:

0.494

AC:

AN:

172

European-Non Finnish (NFE)

AF:

0.438

AC:

25650

AN:

58532

Other (OTH)

AF:

0.367

AC:

566

AN:

1542

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.558

Heterozygous variant carriers

930

1861

2791

3722

4652

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.193

Hom.:

201

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Congenital Muscular Dystrophy, alpha-dystroglycan related

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.1

Splicing

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

Publications

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NM_001101426.4:c.3275_3282delAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over