rs763777257
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_006295.3(VARS1):c.1324C>T(p.Arg442Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,762 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 Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_006295.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VARS1 | NM_006295.3 | c.1324C>T | p.Arg442Ter | stop_gained | 10/30 | ENST00000375663.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VARS1 | ENST00000375663.8 | c.1324C>T | p.Arg442Ter | stop_gained | 10/30 | 1 | NM_006295.3 | P1 | |
VARS1 | ENST00000489979.1 | n.635C>T | non_coding_transcript_exon_variant | 5/5 | 3 | ||||
VARS1 | ENST00000495010.5 | n.867C>T | non_coding_transcript_exon_variant | 7/8 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246974Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134600
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460762Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726700
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Neurodevelopmental disorder with microcephaly, seizures, and cortical atrophy Pathogenic:1
Pathogenic, no assertion criteria provided | research | MyeliNeuroGene Lab, McGill University Health Center Research Institute | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at