chr6-31959193-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PVS1_SupportingPM2
The NM_006929.5(SKIC2):āc.1A>Gā(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000932 in 1,610,038 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 Uncertain significance (ā ).
Frequency
Consequence
NM_006929.5 start_lost
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SKIC2 | NM_006929.5 | c.1A>G | p.Met1? | start_lost | Exon 1 of 28 | ENST00000375394.7 | NP_008860.4 | |
SKIC2 | XM_011514815.4 | c.1A>G | p.Met1? | start_lost | Exon 1 of 25 | XP_011513117.1 | ||
SKIC2 | XM_047419259.1 | c.1A>G | p.Met1? | start_lost | Exon 1 of 25 | XP_047275215.1 | ||
SKIC2 | XM_047419260.1 | c.1A>G | p.Met1? | start_lost | Exon 1 of 24 | XP_047275216.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247254Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 134000
GnomAD4 exome AF: 0.00000960 AC: 14AN: 1457834Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 725360
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change affects the initiator methionine of the SKIV2L mRNA. The next in-frame methionine is located at codon 2. This variant is present in population databases (rs765397497, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with SKIV2L-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at