rs199829701

Variant names:

• chr1-115651261-TCCCC-T
• NM_138959.3:c.-137-14_-137-11delCCCC

Your query was ambiguous. Multiple possible variants found:

• chr1-115651261-TCCCC-T
• chr1-115651261-TCCCC-TCCC
• chr1-115651261-TCCCC-TCCCCC

Variant summary

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

The NM_138959.3(VANGL1):​c.-137-14_-137-11delCCCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000392 in 510,660 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000039 (0 hom.)
• Consequence: VANGL1 NM_138959.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VANGL1	NM_138959.3	c.-137-14_-137-11delCCCC		intron_variant	Intron 1 of 7	ENST00000355485.7	NP_620409.1
VANGL1	NM_001172412.2	c.-137-14_-137-11delCCCC		intron_variant	Intron 1 of 7		NP_001165883.1
VANGL1	NM_001172411.2	c.-137-14_-137-11delCCCC		intron_variant	Intron 1 of 7		NP_001165882.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VANGL1	ENST00000355485.7	c.-137-15_-137-12delCCCC		intron_variant	Intron 1 of 7	1	NM_138959.3	ENSP00000347672.2
VANGL1	ENST00000310260.7	c.-137-15_-137-12delCCCC		intron_variant	Intron 1 of 7	1		ENSP00000310800.3
VANGL1	ENST00000369510.8	c.-137-15_-137-12delCCCC		intron_variant	Intron 1 of 7	1		ENSP00000358523.3
VANGL1	ENST00000369509.1	c.-152_-149delCCCC		upstream_gene_variant		1		ENSP00000358522.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000392 AC: 2 AN: 510660 Hom.: 0 AF XY: 0.00000364 AC XY: 1 AN XY: 274928

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000445

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: 0.00000322

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-116193882;