rs541431101
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_138959.3(VANGL1):c.205-4C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_138959.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VANGL1 | NM_138959.3 | c.205-4C>G | splice_region_variant, intron_variant | Intron 3 of 7 | ENST00000355485.7 | NP_620409.1 | ||
VANGL1 | NM_001172412.2 | c.205-4C>G | splice_region_variant, intron_variant | Intron 3 of 7 | NP_001165883.1 | |||
VANGL1 | NM_001172411.2 | c.199-4C>G | splice_region_variant, intron_variant | Intron 3 of 7 | NP_001165882.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VANGL1 | ENST00000355485.7 | c.205-4C>G | splice_region_variant, intron_variant | Intron 3 of 7 | 1 | NM_138959.3 | ENSP00000347672.2 | |||
VANGL1 | ENST00000310260.7 | c.205-4C>G | splice_region_variant, intron_variant | Intron 3 of 7 | 1 | ENSP00000310800.3 | ||||
VANGL1 | ENST00000369509.1 | c.205-4C>G | splice_region_variant, intron_variant | Intron 2 of 6 | 1 | ENSP00000358522.1 | ||||
VANGL1 | ENST00000369510.8 | c.199-4C>G | splice_region_variant, intron_variant | Intron 3 of 7 | 1 | ENSP00000358523.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250686Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135606
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727222
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at