NM_001101426.4:c.*3276_*3282delAAAAAAA

Variant names:

• chr7-16088412-CTTTTTTT-C
• rs71549971
• NM_001101426.4:c.*3276_*3282delAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_001101426.4(CRPPA):​c.*3276_*3282delAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0038 (1 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: CRPPA NM_001101426.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• 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 Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00378 (427/113110) while in subpopulation SAS AF= 0.00446 (17/3812). AF 95% confidence interval is 0.00285. There are 1 homozygotes in gnomad4. There are 250 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRPPA	NM_001101426.4	c.*3276_*3282delAAAAAAA		3_prime_UTR_variant	Exon 10 of 10	ENST00000407010.7	NP_001094896.1
CRPPA	NM_001368197.1	c.*3276_*3282delAAAAAAA		3_prime_UTR_variant	Exon 9 of 9		NP_001355126.1
CRPPA	NM_001101417.4	c.*3276_*3282delAAAAAAA		3_prime_UTR_variant	Exon 9 of 9		NP_001094887.1
CRPPA	NR_160656.1	n.4697_4703delAAAAAAA		non_coding_transcript_exon_variant	Exon 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRPPA	ENST00000407010	c.*3276_*3282delAAAAAAA		3_prime_UTR_variant	Exon 10 of 10	5	NM_001101426.4	ENSP00000385478.2

Frequencies

GnomAD3 genomes AF: 0.00378 AC: 428 AN: 113118 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.000616

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00263

Gnomad ASJ AF: 0.00954

Gnomad EAS AF: 0.00324

Gnomad SAS AF: 0.00469

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00323

Gnomad OTH AF: 0.00518

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

GnomAD4 genome AF: 0.00378 AC: 427 AN: 113110 Hom.: 1 Cov.: 0 AF XY: 0.00476 AC XY: 250 AN XY: 52522

Gnomad4 AFR AF: 0.000615

Gnomad4 AMR AF: 0.00263

Gnomad4 ASJ AF: 0.00954

Gnomad4 EAS AF: 0.00298

Gnomad4 SAS AF: 0.00446

Gnomad4 FIN AF: 0.0293

Gnomad4 NFE AF: 0.00323

Gnomad4 OTH AF: 0.00579

ClinVar

Not reported in ClinVar

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;