1-115641975-AGCG-A

Variant names:

• chr1-115641975-AGCG-A
• rs886045116
• NM_138959.3:c.-235_-233delCGG

Variant summary

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

The NM_138959.3(VANGL1):​c.-235_-233delCGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000331 in 151,166 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000067 (0 hom., cov: 30)
  • Exomes 𝑓: 0.0034 (0 hom.)
• Consequence: VANGL1 NM_138959.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24

Genes affected

VANGL1 (HGNC:15512): (VANGL planar cell polarity protein 1) This gene encodes a member of the tretraspanin family. The encoded protein may be involved in mediating intestinal trefoil factor induced wound healing in the intestinal mucosa. Mutations in this gene are associated with neural tube defects. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VANGL1	NM_138959.3	c.-235_-233delCGG		5_prime_UTR_variant	Exon 1 of 8	ENST00000355485.7	NP_620409.1
VANGL1	NM_001172411.2	c.-235_-233delCGG		5_prime_UTR_variant	Exon 1 of 8		NP_001165882.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VANGL1	ENST00000355485	c.-235_-233delCGG		5_prime_UTR_variant	Exon 1 of 8	1	NM_138959.3	ENSP00000347672.2
VANGL1	ENST00000369510	c.-235_-233delCGG		5_prime_UTR_variant	Exon 1 of 8	1		ENSP00000358523.3
VANGL1	ENST00000369510.8	c.-235_-233delCGG		non_coding_transcript_variant		1		ENSP00000358523.3
VANGL1	ENST00000369510.8	c.-248_-246delGCG		upstream_gene_variant		1		ENSP00000358523.3

Frequencies

GnomAD3 genomes AF: 0.00000667 AC: 1 AN: 149880 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000662

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00338 AC: 4 AN: 1182 Hom.: 0 AF XY: 0.00300 AC XY: 2 AN XY: 666

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: 0.00283

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000667 AC: 1 AN: 149984 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 73188

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000661

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs886045116; hg19: chr1-116184596;