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NM_032119.4(ADGRV1):c.7176C>T (p.Ser2392=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Sep 23, 2021)
Last evaluated:
Dec 2, 2020
Accession:
VCV000046363.8
Variation ID:
46363
Description:
single nucleotide variant
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NM_032119.4(ADGRV1):c.7176C>T (p.Ser2392=)

Allele ID
55528
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q14.3
Genomic location
5: 90693932 (GRCh38) GRCh38 UCSC
5: 89989749 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.90693932C>T
NG_007083.2:g.169589C>T
NM_032119.4:c.7176C>T MANE Select NP_115495.3:p.Ser2392= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000005.10:90693931:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00280 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00307
Trans-Omics for Precision Medicine (TOPMed) 0.00332
1000 Genomes Project 0.00280
Links
ClinGen: CA138196
dbSNP: rs111033452
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Jul 20, 2015 RCV000039619.8
Benign 4 criteria provided, multiple submitters, no conflicts Dec 2, 2020 RCV000958817.5
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV001154581.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ADGRV1 - - GRCh38
GRCh37
2418 2449

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jul 20, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000332957.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2C
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001315957.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Benign
(Mar 13, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000063308.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Ser2392Ser in exon 33 of GPR98: }: This variant is not expected to have clinical significance because it does not alter an amino acid residue, … (more)
Benign
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001105695.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001907487.1
Submitted: (Sep 21, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 28157192)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001976171.1
Submitted: (Sep 21, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001929063.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000193284.1
Submitted: (Sep 11, 2014)
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001920693.1
Submitted: (Sep 23, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ADGRV1 - - - -

Text-mined citations for rs111033452...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 30, 2021