20-58903579-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000516.7(GNAS):c.306G>T(p.Ala102Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,461,820 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A102A) has been classified as Benign.
Frequency
Consequence
NM_000516.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GNAS | NM_000516.7 | c.306G>T | p.Ala102Ala | synonymous_variant | 4/13 | ENST00000371085.8 | NP_000507.1 | |
GNAS | NM_016592.5 | c.*212G>T | 3_prime_UTR_variant | 4/13 | ENST00000371075.7 | NP_057676.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GNAS | ENST00000371085.8 | c.306G>T | p.Ala102Ala | synonymous_variant | 4/13 | 1 | NM_000516.7 | ENSP00000360126.3 | ||
GNAS | ENST00000676826.2 | c.2238G>T | p.Ala746Ala | synonymous_variant | 4/13 | ENSP00000504675.2 | ||||
GNAS | ENST00000371102.8 | c.2193G>T | p.Ala731Ala | synonymous_variant | 3/12 | 5 | ENSP00000360143.4 | |||
GNAS | ENST00000354359.12 | c.309G>T | p.Ala103Ala | synonymous_variant | 4/13 | 1 | ENSP00000346328.7 | |||
GNAS | ENST00000371095.7 | c.264G>T | p.Ala88Ala | synonymous_variant | 3/12 | 1 | ENSP00000360136.3 | |||
GNAS | ENST00000470512.6 | c.132G>T | p.Ala44Ala | synonymous_variant | 4/13 | 5 | ENSP00000499552.2 | |||
GNAS | ENST00000480232.6 | c.132G>T | p.Ala44Ala | synonymous_variant | 5/14 | 5 | ENSP00000499545.2 | |||
GNAS | ENST00000663479.2 | c.132G>T | p.Ala44Ala | synonymous_variant | 4/13 | ENSP00000499353.2 | ||||
GNAS | ENST00000462499.6 | c.87G>T | p.Ala29Ala | synonymous_variant | 3/12 | 2 | ENSP00000499758.2 | |||
GNAS | ENST00000467227.6 | c.87G>T | p.Ala29Ala | synonymous_variant | 4/13 | 3 | ENSP00000499681.2 | |||
GNAS | ENST00000478585.6 | c.87G>T | p.Ala29Ala | synonymous_variant | 3/12 | 2 | ENSP00000499762.2 | |||
GNAS | ENST00000481039.6 | c.87G>T | p.Ala29Ala | synonymous_variant | 3/12 | 5 | ENSP00000499767.2 | |||
GNAS | ENST00000485673.6 | c.87G>T | p.Ala29Ala | synonymous_variant | 3/12 | 5 | ENSP00000499334.2 | |||
GNAS | ENST00000488546.6 | c.87G>T | p.Ala29Ala | synonymous_variant | 3/12 | 5 | ENSP00000499332.2 | |||
GNAS | ENST00000492907.6 | c.87G>T | p.Ala29Ala | synonymous_variant | 3/12 | 3 | ENSP00000499443.2 | |||
GNAS | ENST00000371075.7 | c.*212G>T | 3_prime_UTR_variant | 4/13 | 1 | NM_016592.5 | ENSP00000360115.3 | |||
GNAS | ENST00000461152.6 | c.*176G>T | 3_prime_UTR_variant | 3/3 | 5 | ENSP00000499274.1 | ||||
GNAS | ENST00000453292.7 | c.*167G>T | 3_prime_UTR_variant | 3/12 | 5 | ENSP00000392000.2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251484Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135916
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461820Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727216
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 03, 2023 | - - |
GNAS-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 13, 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