20-58840113-C-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_016592.5(GNAS):c.7C>G(p.Arg3Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000757 in 1,610,852 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3W) has been classified as Uncertain significance.
Frequency
Consequence
NM_016592.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNAS | NM_016592.5 | c.7C>G | p.Arg3Gly | missense_variant | 1/13 | ENST00000371075.7 | |
GNAS-AS1 | NR_002785.2 | n.819+1824G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNAS | ENST00000371075.7 | c.7C>G | p.Arg3Gly | missense_variant | 1/13 | 1 | NM_016592.5 | ||
GNAS-AS1 | ENST00000424094.6 | n.819+1824G>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152022Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000123 AC: 30AN: 244802Hom.: 0 AF XY: 0.0000897 AC XY: 12AN XY: 133842
GnomAD4 exome AF: 0.0000740 AC: 108AN: 1458830Hom.: 0 Cov.: 35 AF XY: 0.0000799 AC XY: 58AN XY: 725804
GnomAD4 genome ? AF: 0.0000921 AC: 14AN: 152022Hom.: 0 Cov.: 32 AF XY: 0.0000943 AC XY: 7AN XY: 74244
ClinVar
Submissions by phenotype
Pseudohypoparathyroidism type 1B;C2932716:Pseudohypoparathyroidism type 1C;C3494506:Pseudohypoparathyroidism type I A Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Apr 08, 2022 | - - |
GNAS-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 02, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at