1-53509949-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001367484.1(GLIS1):āc.1962G>Cā(p.Gln654His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000691 in 1,303,328 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. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001367484.1 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 |
---|---|---|---|---|---|---|---|
GLIS1 | NM_001367484.1 | c.1962G>C | p.Gln654His | missense_variant | 9/11 | ENST00000628545.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLIS1 | ENST00000628545.2 | c.1962G>C | p.Gln654His | missense_variant | 9/11 | 5 | NM_001367484.1 | P2 | |
GLIS1 | ENST00000312233.4 | c.1437G>C | p.Gln479His | missense_variant | 8/10 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152060Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000507 AC: 5AN: 98662Hom.: 0 AF XY: 0.0000379 AC XY: 2AN XY: 52736
GnomAD4 exome AF: 0.00000608 AC: 7AN: 1151268Hom.: 0 Cov.: 32 AF XY: 0.00000545 AC XY: 3AN XY: 550000
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152060Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74260
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2022 | The c.1437G>C (p.Q479H) alteration is located in exon 8 (coding exon 6) of the GLIS1 gene. This alteration results from a G to C substitution at nucleotide position 1437, causing the glutamine (Q) at amino acid position 479 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at