Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala)

Help
Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
16 (Most recent: Sep 30, 2021)
Last evaluated:
Jul 22, 2021
Accession:
VCV000254953.12
Variation ID:
254953
Description:
single nucleotide variant
Help

NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala)

Allele ID
252982
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q21.3
Genomic location
7: 94413927 (GRCh38) GRCh38 UCSC
7: 94043239 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P08123:p.Pro549Ala
NM_000089.3:c.1645C>G NP_000080.2:p.Pro549Ala missense
NC_000007.13:g.94043239C>G
... more HGVS
Protein change
P549A
Other names
-
Canonical SPDI
NC_000007.14:94413926:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.17832 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.80977
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.79433
The Genome Aggregation Database (gnomAD) 0.80779
Trans-Omics for Precision Medicine (TOPMed) 0.80931
1000 Genomes Project 0.82169
Links
ClinGen: CA4347144
UniProtKB: P08123#VAR_001867
dbSNP: rs42524
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 7 criteria provided, multiple submitters, no conflicts Jul 26, 2017 RCV000244604.8
Benign 2 criteria provided, multiple submitters, no conflicts Jul 22, 2021 RCV000269609.3
Benign 1 criteria provided, single submitter Apr 27, 2017 RCV000323983.2
Benign 1 criteria provided, single submitter May 28, 2019 RCV000987925.1
Benign 1 criteria provided, single submitter Aug 31, 2020 RCV001282168.2
Benign 1 criteria provided, single submitter Dec 6, 2020 RCV001512869.1
Benign 1 criteria provided, single submitter Jul 22, 2021 RCV001589216.1
Benign 1 criteria provided, single submitter Jul 22, 2021 RCV001589218.1
Benign 1 criteria provided, single submitter Jul 22, 2021 RCV001589217.1
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL1A2 No evidence available No evidence available GRCh38
GRCh37
1017 1039

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000302007.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Apr 25, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000538714.1
Submitted: (Apr 03, 2017)
Evidence details
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Benign
(Jul 26, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000612915.1
Submitted: (Aug 17, 2017)
Evidence details
Benign
(Mar 03, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000516229.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Ehlers-Danlos syndrome, classic type I
Allele origin: unknown
Mendelics
Accession: SCV001137419.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Osteogenesis imperfecta
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000470592.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Ehlers-danlos syndrome, arthrochalasia type, 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000470591.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Aug 31, 2020)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001156702.2
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Dec 06, 2020)
criteria provided, single submitter
Method: clinical testing
Osteogenesis imperfecta type I
Ehlers-Danlos syndrome, classic type I
Allele origin: germline
Invitae
Accession: SCV001720359.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Ehlers-danlos syndrome, arthrochalasia type, 2
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001821878.1
Submitted: (Sep 01, 2021)
Evidence details
Benign
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Osteogenesis imperfecta with normal sclerae, dominant form
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001821881.1
Submitted: (Sep 01, 2021)
Evidence details
Benign
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Osteogenesis imperfecta, recessive perinatal lethal
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001821879.1
Submitted: (Sep 01, 2021)
Evidence details
Benign
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Osteogenesis imperfecta type III
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001821880.1
Submitted: (Sep 01, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001808434.1
Submitted: (Aug 24, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001739729.3
Submitted: (Sep 02, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001954506.1
Submitted: (Sep 30, 2021)
Evidence details

Functional evidence

Help
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

Help
There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs42524...

Help
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