16-57659696-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_201525.4(ADGRG1):c.1555+15G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 1,611,888 control chromosomes in the GnomAD database, including 1,273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_201525.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADGRG1 | NM_201525.4 | c.1555+15G>C | intron_variant | Intron 11 of 13 | ENST00000562631.7 | NP_958933.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0173 AC: 2632AN: 152084Hom.: 142 Cov.: 32
GnomAD3 exomes AF: 0.0354 AC: 8687AN: 245728Hom.: 565 AF XY: 0.0348 AC XY: 4655AN XY: 133770
GnomAD4 exome AF: 0.0135 AC: 19663AN: 1459684Hom.: 1130 Cov.: 35 AF XY: 0.0148 AC XY: 10735AN XY: 726100
GnomAD4 genome AF: 0.0174 AC: 2643AN: 152204Hom.: 143 Cov.: 32 AF XY: 0.0213 AC XY: 1587AN XY: 74418
ClinVar
Submissions by phenotype
not specified Benign:3
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Benign:2
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Bilateral frontoparietal polymicrogyria Benign:1
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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at