rs142647500

Variant names:

• chr7-16308637-AAACAAC-A
• rs142647500
• NM_001101426.4:c.685-16_685-11delGTTGTT

Your query was ambiguous. Multiple possible variants found:

• chr7-16308637-AAACAAC-A
• chr7-16308637-AAACAAC-AAAC
• chr7-16308637-AAACAAC-AAACAACAAC
• chr7-16308637-AAACAAC-AAACAACAACAAC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_001101426.4(CRPPA):​c.685-16_685-11delGTTGTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CRPPA NM_001101426.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.23

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 7-16308637-AAACAAC-A is Benign according to our data. Variant chr7-16308637-AAACAAC-A is described in ClinVar as [Likely_benign]. Clinvar id is 3758602.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRPPA	NM_001101426.4	c.685-16_685-11delGTTGTT		intron_variant	Intron 3 of 9	ENST00000407010.7	NP_001094896.1
CRPPA	NM_001368197.1	c.685-7177_685-7172delGTTGTT		intron_variant	Intron 3 of 8		NP_001355126.1
CRPPA	NM_001101417.4	c.535-16_535-11delGTTGTT		intron_variant	Intron 2 of 8		NP_001094887.1
CRPPA	NR_160656.1	n.901-30417_901-30412delGTTGTT		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRPPA	ENST00000407010.7	c.685-16_685-11delGTTGTT		intron_variant	Intron 3 of 9	5	NM_001101426.4	ENSP00000385478.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1254068 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 633188

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7;C5190987:Autosomal recessive limb-girdle muscular dystrophy type 2U Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 13, 2025

- -

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: rs142647500; hg19: chr7-16348262;