chr1-115663704-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PP3_ModerateBP6_ModerateBS2
The NM_138959.3(VANGL1):c.248C>T(p.Ser83Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000052 in 1,614,170 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. S83S) has been classified as Likely benign.
Frequency
Consequence
NM_138959.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VANGL1 | NM_138959.3 | c.248C>T | p.Ser83Leu | missense_variant | Exon 4 of 8 | ENST00000355485.7 | NP_620409.1 | |
VANGL1 | NM_001172412.2 | c.248C>T | p.Ser83Leu | missense_variant | Exon 4 of 8 | NP_001165883.1 | ||
VANGL1 | NM_001172411.2 | c.242C>T | p.Ser81Leu | missense_variant | Exon 4 of 8 | NP_001165882.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VANGL1 | ENST00000355485.7 | c.248C>T | p.Ser83Leu | missense_variant | Exon 4 of 8 | 1 | NM_138959.3 | ENSP00000347672.2 | ||
VANGL1 | ENST00000310260.7 | c.248C>T | p.Ser83Leu | missense_variant | Exon 4 of 8 | 1 | ENSP00000310800.3 | |||
VANGL1 | ENST00000369509.1 | c.248C>T | p.Ser83Leu | missense_variant | Exon 3 of 7 | 1 | ENSP00000358522.1 | |||
VANGL1 | ENST00000369510.8 | c.242C>T | p.Ser81Leu | missense_variant | Exon 4 of 8 | 1 | ENSP00000358523.3 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251400Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135900
GnomAD4 exome AF: 0.0000458 AC: 67AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727246
GnomAD4 genome AF: 0.000112 AC: 17AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74458
ClinVar
Submissions by phenotype
Neural tube defect Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at