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NM_025074.7(FRAS1):c.9806G>A (p.Arg3269Gln)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
11
First in ClinVar:
Jun 28, 2015
Most recent Submission:
Jan 21, 2023
Last evaluated:
Jun 9, 2022
Accession:
VCV000198348.26
Variation ID:
198348
Description:
single nucleotide variant
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NM_025074.7(FRAS1):c.9806G>A (p.Arg3269Gln)

Allele ID
195509
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
4q21.21
Genomic location
4: 78511299 (GRCh38) GRCh38 UCSC
4: 79432453 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_025074.7:c.9806G>A MANE Select NP_079350.5:p.Arg3269Gln missense
NC_000004.12:g.78511299G>A
NC_000004.11:g.79432453G>A
... more HGVS
Protein change
R3269Q
Other names
-
Canonical SPDI
NC_000004.12:78511298:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00140 (A)

Allele frequency
1000 Genomes Project 0.00140
Exome Aggregation Consortium (ExAC) 0.00567
The Genome Aggregation Database (gnomAD) 0.00526
The Genome Aggregation Database (gnomAD) 0.00592
Trans-Omics for Precision Medicine (TOPMed) 0.00581
The Genome Aggregation Database (gnomAD), exomes 0.00518
Trans-Omics for Precision Medicine (TOPMed) 0.00628
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00695
Links
ClinGen: CA203377
dbSNP: rs61729366
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 Jun 9, 2022 RCV000179644.10
Likely benign 3 criteria provided, multiple submitters, no conflicts Apr 3, 2022 RCV000315339.7
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 16, 2021 RCV000872220.15
risk factor 1 no assertion criteria provided Nov 9, 2016 RCV000577951.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FRAS1 - - GRCh38
GRCh37
872 899

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Likely benign
(Sep 14, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Affected status: no
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000594881.1
First in ClinVar: Jun 28, 2015
Last updated: Jun 28, 2015
Benign
(Jan 21, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Affected status: unknown
Allele origin: germline
Eurofins NTD LLC (GA)
Accession: SCV000231924.5
First in ClinVar: Jun 28, 2015
Last updated: May 03, 2018
Other databases
http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=FRAS1
http://www.ncbi.nlm.nih.gov/vari… http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/?chr=4&from=79432453&to=79432453
Number of individuals with the variant: 2
Zygosity: 2 Single Heterozygote
Sex: mixed
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Fraser syndrome 1
Affected status: unknown
Allele origin: germline
Illumina Laboratory Services,Illumina
Accession: SCV000451296.3
First in ClinVar: Dec 06, 2016
Last updated: May 31, 2020
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
(Dec 16, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001014005.3
First in ClinVar: Dec 17, 2019
Last updated: May 16, 2022
Benign
(Jun 09, 2022)
criteria provided, single submitter
Method: clinical testing
not specified
Affected status: unknown
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002555803.1
First in ClinVar: Aug 08, 2022
Last updated: Aug 08, 2022
Comment:
Variant summary: FRAS1 c.9806G>A (p.Arg3269Gln) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging … (more)
Likely benign
(Apr 03, 2022)
criteria provided, single submitter
Method: clinical testing
Fraser syndrome 1
Affected status: unknown
Allele origin: unknown
Fulgent Genetics, Fulgent Genetics
Accession: SCV002802550.1
First in ClinVar: Dec 31, 2022
Last updated: Dec 31, 2022
Likely benign
(Nov 01, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: yes
Allele origin: germline
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001502463.10
First in ClinVar: Mar 14, 2021
Last updated: Jan 21, 2023
Number of individuals with the variant: 1
risk factor
(Nov 09, 2016)
no assertion criteria provided
Method: research
Congenital diaphragmatic hernia
Affected status: yes
Allele origin: inherited
Daryl Scott Lab,Baylor College of Medicine
Accession: SCV000484668.1
First in ClinVar: Jan 28, 2018
Last updated: Jan 28, 2018
Clinical Features:
Ventricular septal defect (present) , Pectus excavatum (present) , Bilateral hydronephrosis (present) , Cryptorchidism (present) , Inguinal hernia (present)
Zygosity: 1 Single Heterozygote
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
Fraser syndrome 1
Affected status: yes
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV000734360.1
First in ClinVar: Apr 09, 2018
Last updated: Apr 09, 2018
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Affected status: yes
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001798770.1
First in ClinVar: Aug 21, 2021
Last updated: Aug 21, 2021
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Affected status: yes
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: SCV001929395.1
First in ClinVar: Sep 24, 2021
Last updated: Sep 24, 2021

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.

Text-mined citations for rs61729366...

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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 Jan 21, 2023