1-115659672-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_138959.3(VANGL1):c.103C>T(p.Arg35Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,613,928 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 Uncertain significance (★).
Frequency
Consequence
NM_138959.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VANGL1 | NM_138959.3 | c.103C>T | p.Arg35Trp | missense_variant | Exon 3 of 8 | ENST00000355485.7 | NP_620409.1 | |
VANGL1 | NM_001172412.2 | c.103C>T | p.Arg35Trp | missense_variant | Exon 3 of 8 | NP_001165883.1 | ||
VANGL1 | NM_001172411.2 | c.103C>T | p.Arg35Trp | missense_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.103C>T | p.Arg35Trp | missense_variant | Exon 3 of 8 | 1 | NM_138959.3 | ENSP00000347672.2 | ||
VANGL1 | ENST00000310260.7 | c.103C>T | p.Arg35Trp | missense_variant | Exon 3 of 8 | 1 | ENSP00000310800.3 | |||
VANGL1 | ENST00000369509.1 | c.103C>T | p.Arg35Trp | missense_variant | Exon 2 of 7 | 1 | ENSP00000358522.1 | |||
VANGL1 | ENST00000369510.8 | c.103C>T | p.Arg35Trp | missense_variant | Exon 3 of 8 | 1 | ENSP00000358523.3 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152038Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251436Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135890
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727244
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74250
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.103C>T (p.R35W) alteration is located in exon 3 (coding exon 2) of the VANGL1 gene. This alteration results from a C to T substitution at nucleotide position 103, causing the arginine (R) at amino acid position 35 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at