rs41304884
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_032119.4(ADGRV1):āc.16164A>Gā(p.Arg5388=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0169 in 1,566,476 control chromosomes in the GnomAD database, including 329 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.014 ( 17 hom., cov: 32)
Exomes š: 0.017 ( 312 hom. )
Consequence
ADGRV1
NM_032119.4 synonymous
NM_032119.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.885
Genes affected
ADGRV1 (HGNC:17416): (adhesion G protein-coupled receptor V1) This gene encodes a member of the G-protein coupled receptor superfamily. The encoded protein contains a 7-transmembrane receptor domain, binds calcium and is expressed in the central nervous system. Mutations in this gene are associated with Usher syndrome 2 and familial febrile seizures. Several alternatively spliced transcripts have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 5-90815704-A-G is Benign according to our data. Variant chr5-90815704-A-G is described in ClinVar as [Benign]. Clinvar id is 46283.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-90815704-A-G is described in Lovd as [Likely_benign]. Variant chr5-90815704-A-G is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-0.885 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0137 (2087/152280) while in subpopulation SAS AF= 0.0483 (233/4826). AF 95% confidence interval is 0.0432. There are 17 homozygotes in gnomad4. There are 1043 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 17 AR,Digenic gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRV1 | NM_032119.4 | c.16164A>G | p.Arg5388= | synonymous_variant | 75/90 | ENST00000405460.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.16164A>G | p.Arg5388= | synonymous_variant | 75/90 | 1 | NM_032119.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0137 AC: 2092AN: 152162Hom.: 17 Cov.: 32
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GnomAD3 exomes AF: 0.0171 AC: 3139AN: 184080Hom.: 47 AF XY: 0.0193 AC XY: 1883AN XY: 97506
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GnomAD4 exome AF: 0.0172 AC: 24315AN: 1414196Hom.: 312 Cov.: 27 AF XY: 0.0182 AC XY: 12725AN XY: 699588
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GnomAD4 genome AF: 0.0137 AC: 2087AN: 152280Hom.: 17 Cov.: 32 AF XY: 0.0140 AC XY: 1043AN XY: 74468
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 27, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 10, 2013 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | Arg5388Arg in exon 75 of GPR98: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, has been identified in 0.2% (13/6503) of Europe an American chromosomes and 0.8% (27/3116) of African American chromosomes from a broad population by the NHLBI Exome sequencing project (http://evs.gs.washingt on.edu/EVS/; dbSNP rs41304884), and is reported as benign (Le Quesne Stabel 201 2). - |
Usher syndrome type 2C Benign:1
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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at