rs201236317
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_032119.4(ADGRV1):c.1033C>A(p.Gln345Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000625 in 1,613,694 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. Q345Q) has been classified as Likely benign.
Frequency
Consequence
NM_032119.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRV1 | NM_032119.4 | c.1033C>A | p.Gln345Lys | missense_variant | 7/90 | ENST00000405460.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.1033C>A | p.Gln345Lys | missense_variant | 7/90 | 1 | NM_032119.4 | P1 | |
ADGRV1 | ENST00000640281.1 | n.1092C>A | non_coding_transcript_exon_variant | 7/7 | 1 | ||||
ADGRV1 | ENST00000640083.1 | n.738C>A | non_coding_transcript_exon_variant | 5/6 | 5 | ||||
ADGRV1 | ENST00000640109.1 | n.1129C>A | non_coding_transcript_exon_variant | 7/9 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000717 AC: 109AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000855 AC: 213AN: 249052Hom.: 0 AF XY: 0.000792 AC XY: 107AN XY: 135100
GnomAD4 exome AF: 0.000615 AC: 899AN: 1461580Hom.: 2 Cov.: 32 AF XY: 0.000620 AC XY: 451AN XY: 727076
GnomAD4 genome ? AF: 0.000717 AC: 109AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.000929 AC XY: 69AN XY: 74292
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:4
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 23, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 12, 2016 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 19, 2015 | p.Gln345Lys in exon 7 of GPR98: This variant is not expected to have clinical si gnificance because it has been identified in 0.2% (135/66722) of European chromo somes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs201236317), and the glutamine (Gln) residue at position 345 is not evol utionarily conserved across species, with many species having a lysine (Lys) at this position. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at