chr6-31779038-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_006295.3(VARS1):c.3655C>T(p.Arg1219Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,612,740 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1219Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_006295.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VARS1 | NM_006295.3 | c.3655C>T | p.Arg1219Trp | missense_variant | 29/30 | ENST00000375663.8 | |
VARS1 | XM_005249362.3 | c.3658C>T | p.Arg1220Trp | missense_variant | 29/30 | ||
VARS1 | XM_047419296.1 | c.3658C>T | p.Arg1220Trp | missense_variant | 28/29 | ||
VARS1 | XM_047419297.1 | c.3655C>T | p.Arg1219Trp | missense_variant | 28/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VARS1 | ENST00000375663.8 | c.3655C>T | p.Arg1219Trp | missense_variant | 29/30 | 1 | NM_006295.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000164 AC: 4AN: 243570Hom.: 0 AF XY: 0.0000300 AC XY: 4AN XY: 133344
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460524Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 726572
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74376
ClinVar
Submissions by phenotype
Neurodevelopmental disorder with microcephaly, seizures, and cortical atrophy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | May 19, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at