rs149607882
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_201525.4(ADGRG1):c.402G>A(p.Pro134=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000917 in 1,614,046 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P134P) has been classified as Likely benign.
Frequency
Consequence
NM_201525.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRG1 | NM_201525.4 | c.402G>A | p.Pro134= | synonymous_variant | 3/14 | ENST00000562631.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRG1 | ENST00000562631.7 | c.402G>A | p.Pro134= | synonymous_variant | 3/14 | 1 | NM_201525.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152198Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251334Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135852
GnomAD4 exome AF: 0.0000896 AC: 131AN: 1461848Hom.: 1 Cov.: 32 AF XY: 0.0000853 AC XY: 62AN XY: 727222
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152198Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74360
ClinVar
Submissions by phenotype
Bilateral frontoparietal polymicrogyria Uncertain:1
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. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 30, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
ADGRG1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 22, 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