chr1-115659723-ACT-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_138959.3(VANGL1):c.155_156del(p.Thr52ArgfsTer8) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000657 in 152,124 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Consequence
VANGL1
NM_138959.3 frameshift
NM_138959.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.22
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 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| VANGL1 | NM_138959.3 | c.155_156del | p.Thr52ArgfsTer8 | frameshift_variant | 3/8 | ENST00000355485.7 | |
| VANGL1 | NM_001172411.2 | c.155_156del | p.Thr52ArgfsTer8 | frameshift_variant | 3/8 | ||
| VANGL1 | NM_001172412.2 | c.155_156del | p.Thr52ArgfsTer8 | frameshift_variant | 3/8 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| VANGL1 | ENST00000355485.7 | c.155_156del | p.Thr52ArgfsTer8 | frameshift_variant | 3/8 | 1 | NM_138959.3 | P3 | |
| VANGL1 | ENST00000310260.7 | c.155_156del | p.Thr52ArgfsTer8 | frameshift_variant | 3/8 | 1 | P3 | ||
| VANGL1 | ENST00000369509.1 | c.155_156del | p.Thr52ArgfsTer8 | frameshift_variant | 2/7 | 1 | P3 | ||
| VANGL1 | ENST00000369510.8 | c.155_156del | p.Thr52ArgfsTer8 | frameshift_variant | 3/8 | 1 | A1 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74316
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Uncertain:1
| Uncertain significance, no assertion criteria provided | research | Gharavi Laboratory, Columbia University | Sep 16, 2018 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at