rs200720013
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_032575.3(GLIS2):c.1105G>A(p.Gly369Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000454 in 1,569,222 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032575.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLIS2 | NM_032575.3 | c.1105G>A | p.Gly369Ser | missense_variant | 7/7 | ENST00000433375.2 | |
GLIS2 | NM_001318918.2 | c.1105G>A | p.Gly369Ser | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLIS2 | ENST00000433375.2 | c.1105G>A | p.Gly369Ser | missense_variant | 7/7 | 1 | NM_032575.3 | P1 | |
ENST00000574705.1 | n.765C>T | non_coding_transcript_exon_variant | 1/1 | ||||||
GLIS2 | ENST00000262366.7 | c.1105G>A | p.Gly369Ser | missense_variant | 8/8 | 2 | P1 | ||
PAM16 | ENST00000577031.5 | c.291+3866C>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000572 AC: 87AN: 152166Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.000937 AC: 162AN: 172802Hom.: 0 AF XY: 0.000763 AC XY: 73AN XY: 95710
GnomAD4 exome AF: 0.000441 AC: 625AN: 1416938Hom.: 0 Cov.: 35 AF XY: 0.000431 AC XY: 303AN XY: 702296
GnomAD4 genome ? AF: 0.000571 AC: 87AN: 152284Hom.: 1 Cov.: 34 AF XY: 0.000551 AC XY: 41AN XY: 74456
ClinVar
Submissions by phenotype
Nephronophthisis 7 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Nephronophthisis Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at