rs201354921
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001048166.1(STIL):c.3157G>A(p.Gly1053Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000097 in 1,607,482 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 (★★).
Frequency
Consequence
NM_001048166.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000739 AC: 18AN: 243496Hom.: 0 AF XY: 0.000114 AC XY: 15AN XY: 131608
GnomAD4 exome AF: 0.0000941 AC: 137AN: 1455218Hom.: 0 Cov.: 33 AF XY: 0.000105 AC XY: 76AN XY: 723560
GnomAD4 genome AF: 0.000125 AC: 19AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74456
ClinVar
Submissions by phenotype
Microcephaly 7, primary, autosomal recessive Uncertain:1
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not provided Uncertain:1
This variant has not been reported in the literature in individuals affected with STIL-related conditions. This variant is present in population databases (rs201354921, gnomAD 0.02%). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 1052 of the STIL protein (p.Gly1052Ser). ClinVar contains an entry for this variant (Variation ID: 160062). 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt STIL protein function. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at