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NM_032119.4(ADGRV1):c.7874G>A (p.Arg2625His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Sep 26, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000046381.7
Variation ID:
46381
Description:
single nucleotide variant
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NM_032119.4(ADGRV1):c.7874G>A (p.Arg2625His)

Allele ID
55546
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q14.3
Genomic location
5: 90694630 (GRCh38) GRCh38 UCSC
5: 89990447 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.9:g.89990447G>A
LRG_1095:g.170287G>A
LRG_1095t1:c.7874G>A LRG_1095p1:p.Arg2625His
... more HGVS
Protein change
R2625H
Other names
-
Canonical SPDI
NC_000005.10:90694629:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (A)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00226
1000 Genomes Project 0.00060
Trans-Omics for Precision Medicine (TOPMed) 0.00189
The Genome Aggregation Database (gnomAD) 0.00108
The Genome Aggregation Database (gnomAD) 0.00187
Trans-Omics for Precision Medicine (TOPMed) 0.00191
Exome Aggregation Consortium (ExAC) 0.00234
The Genome Aggregation Database (gnomAD), exomes 0.00250
Links
ClinGen: CA138228
dbSNP: rs201214794
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 3 criteria provided, multiple submitters, no conflicts Dec 5, 2017 RCV000039637.7
Benign/Likely benign 5 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000434012.6
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV001157106.1
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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
2423 2454

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Feb 09, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000229674.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001117428.3
Submitted: (Jan 07, 2021)
Evidence details
Likely Benign
(Sep 15, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000511770.1
Submitted: (Feb 17, 2017)
Evidence details
Comment:
Converted during submission to Likely benign.
Benign
(Dec 05, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000063326.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Arg2625His in exon 33 of ADGRV1: This variant is not expected to have clinical significance because it has been identified in 3% (300/10076) of Ashkenazi … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2C
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001318652.1
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
(Feb 25, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000717875.2
Submitted: (Sep 26, 2021)
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: SCV001919046.1
Submitted: (Sep 23, 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: SCV001932092.1
Submitted: (Sep 23, 2021)
Evidence details
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: SCV001968457.1
Submitted: (Sep 21, 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 rs201214794...

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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 Nov 27, 2021