chr5-90558869-CCGGCGGGGACCGCCGGGA-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BS1_Supporting
The NM_032119.4(ADGRV1):c.-26_-9delCGGCGGGGACCGCCGGGA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000462 in 1,559,994 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032119.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152068Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000121 AC: 20AN: 164926Hom.: 0 AF XY: 0.000114 AC XY: 10AN XY: 88024
GnomAD4 exome AF: 0.0000497 AC: 70AN: 1407810Hom.: 0 AF XY: 0.0000446 AC XY: 31AN XY: 695112
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74406
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.-26_-9del in the 5' UTR of GPR98 has not previously been identified in ind ividual's with hearing loss, but has been identified in 6/8296 European chromoso mes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. This variant is located in the 5' untranslated region (UTR) and variants in regulatory regions could have an effe ct on transcriptional or translational efficiency. In summary, the clinical sign ificance of the c.-26_-9del variant is uncertain. -
ADGRV1-related disorder Benign:1
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