6-30914905-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_020442.6(VARS2):c.69C>G(p.Pro23=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,612,970 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P23P) has been classified as Likely benign.
Frequency
Consequence
NM_020442.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VARS2 | NM_020442.6 | c.69C>G | p.Pro23= | synonymous_variant | 2/30 | ENST00000676266.1 | |
VARS2 | NM_001167734.2 | c.159C>G | p.Pro53= | synonymous_variant | 2/30 | ||
VARS2 | NM_001167733.3 | c.-219-251C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VARS2 | ENST00000676266.1 | c.69C>G | p.Pro23= | synonymous_variant | 2/30 | NM_020442.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246602Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134426
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460774Hom.: 0 Cov.: 59 AF XY: 0.00000413 AC XY: 3AN XY: 726702
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74346
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 03, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at