chr7-16102621-A-G

Position:

• chr7-16102621-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001101426.4(CRPPA):​c.1252-10822T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 151,798 control chromosomes in the GnomAD database, including 48,457 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (48457 hom., cov: 32)
• Consequence: CRPPA NM_001101426.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRPPA	NM_001101426.4	c.1252-10822T>C		intron_variant		ENST00000407010.7	NP_001094896.1
CRPPA	NM_001101417.4	c.1102-10822T>C		intron_variant			NP_001094887.1
CRPPA	NM_001368197.1	c.1147-10822T>C		intron_variant			NP_001355126.1
CRPPA	NR_160656.1	n.1317-10822T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRPPA	ENST00000407010.7	c.1252-10822T>C		intron_variant		5	NM_001101426.4	ENSP00000385478	P1
CRPPA	ENST00000399310.3	c.1102-10822T>C		intron_variant		1		ENSP00000382249
CRPPA	ENST00000675257.1	c.844-10822T>C		intron_variant				ENSP00000501664
CRPPA	ENST00000676325.1	c.949-10822T>C		intron_variant				ENSP00000502074

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119461 AN: 151680 Hom.: 48429 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.787 AC: 119532 AN: 151798 Hom.: 48457 Cov.: 32 AF XY: 0.792 AC XY: 58752 AN XY: 74174

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.924

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.813

Alfa AF: 0.787 Hom.: 2647

Bravo AF: 0.779

Asia WGS AF: 0.845 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.7
DANN	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7798339; hg19: chr7-16142246;