16-57654006-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000562631.7(ADGRG1):c.641C>T(p.Ser214Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000609 in 1,614,066 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S214W) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000562631.7 missense
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADGRG1 | NM_201525.4 | c.641C>T | p.Ser214Leu | missense_variant | 5/14 | ENST00000562631.7 | NP_958933.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADGRG1 | ENST00000562631.7 | c.641C>T | p.Ser214Leu | missense_variant | 5/14 | 1 | NM_201525.4 | ENSP00000455351 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00328 AC: 499AN: 152176Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000827 AC: 208AN: 251416Hom.: 0 AF XY: 0.000640 AC XY: 87AN XY: 135890
GnomAD4 exome AF: 0.000331 AC: 484AN: 1461772Hom.: 6 Cov.: 34 AF XY: 0.000265 AC XY: 193AN XY: 727180
GnomAD4 genome AF: 0.00328 AC: 499AN: 152294Hom.: 4 Cov.: 32 AF XY: 0.00321 AC XY: 239AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 06, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 22, 2017 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Bilateral frontoparietal polymicrogyria Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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 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. - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 18, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at