1-115659707-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_138959.3(VANGL1):c.138C>T(p.Val46Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,614,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_138959.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VANGL1 | NM_138959.3 | c.138C>T | p.Val46Val | synonymous_variant | Exon 3 of 8 | ENST00000355485.7 | NP_620409.1 | |
VANGL1 | NM_001172412.2 | c.138C>T | p.Val46Val | synonymous_variant | Exon 3 of 8 | NP_001165883.1 | ||
VANGL1 | NM_001172411.2 | c.138C>T | p.Val46Val | synonymous_variant | Exon 3 of 8 | NP_001165882.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VANGL1 | ENST00000355485.7 | c.138C>T | p.Val46Val | synonymous_variant | Exon 3 of 8 | 1 | NM_138959.3 | ENSP00000347672.2 | ||
VANGL1 | ENST00000310260.7 | c.138C>T | p.Val46Val | synonymous_variant | Exon 3 of 8 | 1 | ENSP00000310800.3 | |||
VANGL1 | ENST00000369509.1 | c.138C>T | p.Val46Val | synonymous_variant | Exon 2 of 7 | 1 | ENSP00000358522.1 | |||
VANGL1 | ENST00000369510.8 | c.138C>T | p.Val46Val | synonymous_variant | Exon 3 of 8 | 1 | ENSP00000358523.3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251456Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135896
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000344 AC XY: 25AN XY: 727244
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
VANGL1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at