7-16441663-C-T

Position:

• chr7-16441663-C-T

Variant summary

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

The XR_007060223.1(LOC105375168):​n.410+7276C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.026 in 152,070 control chromosomes in the GnomAD database, including 70 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 0.026 (70 hom., cov: 32)
• Consequence: LOC105375168 XR_007060223.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

LOC105375168 (HGNC:):

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375168	XR_007060223.1	n.410+7276C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRPPA	ENST00000674759.1	c.-46-35326G>A		intron_variant				ENSP00000502749
CRPPA	ENST00000675257.1	c.-46-35326G>A		intron_variant				ENSP00000501664

Frequencies

GnomAD3 genomes AF: 0.0260 AC: 3956 AN: 151952 Hom.: 70 Cov.: 32

Gnomad AFR AF: 0.0364

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0142

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0159

Gnomad OTH AF: 0.0259

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

GnomAD4 genome AF: 0.0260 AC: 3958 AN: 152070 Hom.: 70 Cov.: 32 AF XY: 0.0272 AC XY: 2024 AN XY: 74338

Gnomad4 AFR AF: 0.0364

Gnomad4 AMR AF: 0.0142

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.0336

Gnomad4 FIN AF: 0.0270

Gnomad4 NFE AF: 0.0159

Gnomad4 OTH AF: 0.0270

Alfa AF: 0.0195 Hom.: 23

Bravo AF: 0.0262

Asia WGS AF: 0.0830 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1921832; hg19: chr7-16481288;