6-31959301-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_006929.5(SKIC2):c.27A>G(p.Leu9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. L9L) has been classified as Likely benign.
Frequency
Consequence
NM_006929.5 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 |
---|---|---|---|---|---|---|---|
SKIC2 | NM_006929.5 | c.27A>G | p.Leu9= | synonymous_variant | 2/28 | ENST00000375394.7 | |
SKIC2 | XM_011514815.4 | c.27A>G | p.Leu9= | synonymous_variant | 2/25 | ||
SKIC2 | XM_047419259.1 | c.27A>G | p.Leu9= | synonymous_variant | 2/25 | ||
SKIC2 | XM_047419260.1 | c.27A>G | p.Leu9= | synonymous_variant | 2/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SKIC2 | ENST00000375394.7 | c.27A>G | p.Leu9= | synonymous_variant | 2/28 | 1 | NM_006929.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.