rs373069459
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_ModerateBP6_Very_Strong
The NM_032119.4(ADGRV1):c.8088G>A(p.Leu2696=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000327 in 1,613,360 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L2696L) has been classified as Likely benign.
Frequency
Consequence
NM_032119.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRV1 | NM_032119.4 | c.8088G>A | p.Leu2696= | synonymous_variant | 34/90 | ENST00000405460.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.8088G>A | p.Leu2696= | synonymous_variant | 34/90 | 1 | NM_032119.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00164 AC: 249AN: 152066Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000498 AC: 124AN: 248928Hom.: 0 AF XY: 0.000378 AC XY: 51AN XY: 135024
GnomAD4 exome AF: 0.000190 AC: 278AN: 1461176Hom.: 0 Cov.: 31 AF XY: 0.000164 AC XY: 119AN XY: 726878
GnomAD4 genome ? AF: 0.00164 AC: 249AN: 152184Hom.: 1 Cov.: 32 AF XY: 0.00149 AC XY: 111AN XY: 74396
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 01, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 14, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | Leu2696Leu in Exon 34 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, and has been identified in 0.6% (20/3106) of Af rican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS). - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 10, 2015 | - - |
ADGRV1-related condition Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 30, 2019 | 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