chr1-115642000-C-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_138959.3(VANGL1):c.-224C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 151,386 control chromosomes in the GnomAD database, including 1,325 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_138959.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VANGL1 | NM_138959.3 | c.-224C>A | 5_prime_UTR_variant | Exon 1 of 8 | ENST00000355485.7 | NP_620409.1 | ||
VANGL1 | NM_001172411.2 | c.-224C>A | 5_prime_UTR_variant | Exon 1 of 8 | NP_001165882.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.117 AC: 17623AN: 150272Hom.: 1281 Cov.: 30
GnomAD4 exome AF: 0.243 AC: 244AN: 1006Hom.: 45 Cov.: 0 AF XY: 0.214 AC XY: 120AN XY: 560
GnomAD4 genome AF: 0.117 AC: 17633AN: 150380Hom.: 1280 Cov.: 30 AF XY: 0.126 AC XY: 9272AN XY: 73432
ClinVar
Submissions by phenotype
not provided Benign:1
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Sacral defect with anterior meningocele Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Neural tube defect Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at