rs142520878
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020442.6(VARS2):āc.2500C>Gā(p.Arg834Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,232 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R834C) has been classified as Likely benign.
Frequency
Consequence
NM_020442.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VARS2 | NM_020442.6 | c.2500C>G | p.Arg834Gly | missense_variant | 26/30 | ENST00000676266.1 | |
VARS2 | NM_001167734.2 | c.2590C>G | p.Arg864Gly | missense_variant | 26/30 | ||
VARS2 | NM_001167733.3 | c.2080C>G | p.Arg694Gly | missense_variant | 25/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VARS2 | ENST00000676266.1 | c.2500C>G | p.Arg834Gly | missense_variant | 26/30 | NM_020442.6 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000410 AC: 1AN: 243656Hom.: 0 AF XY: 0.00000750 AC XY: 1AN XY: 133310
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460232Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726416
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at