rs886045116
Your query was ambiguous. Multiple possible variants found:
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
NM_138959.3 5_prime_UTR
Scores
Not classified
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]
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ACMG classification
Classification made for transcript
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: 1AN: 149880Hom.: 0 Cov.: 30
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GnomAD4 exome AF: 0.00338 AC: 4AN: 1182Hom.: 0 AF XY: 0.00300 AC XY: 2AN XY: 666
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GnomAD4 genome AF: 0.00000667 AC: 1AN: 149984Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 73188
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at