chr16-57628720-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_201525.4(ADGRG1):c.-118C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0162 in 985,510 control chromosomes in the GnomAD database, including 315 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.026 ( 136 hom., cov: 33)
Exomes 𝑓: 0.014 ( 179 hom. )
Consequence
ADGRG1
NM_201525.4 5_prime_UTR
NM_201525.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.355
Genes affected
ADGRG1 (HGNC:4512): (adhesion G protein-coupled receptor G1) This gene encodes a member of the G protein-coupled receptor family and regulates brain cortical patterning. The encoded protein binds specifically to transglutaminase 2, a component of tissue and tumor stroma implicated as an inhibitor of tumor progression. Mutations in this gene are associated with a brain malformation known as bilateral frontoparietal polymicrogyria. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 16-57628720-C-G is Benign according to our data. Variant chr16-57628720-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1254855.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRG1 | NM_201525.4 | c.-118C>G | 5_prime_UTR_variant | 1/14 | ENST00000562631.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRG1 | ENST00000562631.7 | c.-118C>G | 5_prime_UTR_variant | 1/14 | 1 | NM_201525.4 | P4 | ||
ENST00000563251.1 | n.274-1431G>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0264 AC: 4015AN: 152208Hom.: 133 Cov.: 33
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GnomAD4 exome AF: 0.0144 AC: 11978AN: 833184Hom.: 179 Cov.: 31 AF XY: 0.0142 AC XY: 5474AN XY: 384768
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GnomAD4 genome ? AF: 0.0265 AC: 4033AN: 152326Hom.: 136 Cov.: 33 AF XY: 0.0280 AC XY: 2083AN XY: 74490
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at