7-16088412-CTTTTTTTT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001101426.4(CRPPA):c.*3275_*3282del 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.13

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]

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
CRPPA	NM_001101426.4	c.*3275_*3282del		3_prime_UTR_variant	10/10	ENST00000407010.7
CRPPA	NM_001101417.4	c.*3275_*3282del		3_prime_UTR_variant	9/9
CRPPA	NM_001368197.1	c.*3275_*3282del		3_prime_UTR_variant	9/9
CRPPA	NR_160656.1	n.4696_4703del		non_coding_transcript_exon_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRPPA	ENST00000407010.7	c.*3275_*3282del		3_prime_UTR_variant	10/10	5	NM_001101426.4	P1

Frequencies

GnomAD3 genomes AF: 0.375 AC: 42444 AN: 113208 Hom.: 7435 Cov.: 0

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.: 0 AF XY: 0.384 AC XY: 20170 AN XY: 52580

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.367

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital Muscular Dystrophy, alpha-dystroglycan related Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71549971; hg19: chr7-16128037;